diff --git a/CHANGES.md b/CHANGES.md
index 80a3bb1f667..468ef1408d7 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -8,5 +8,6 @@ Apollo 2.0.1
 * [Upgrade spring boot to fix search user issue](https://github.com/apolloconfig/apollo/pull/4366)
 * [Fix search user duplication issue](https://github.com/apolloconfig/apollo/pull/4371)
 * [Fix the npe issue for old version of gray release rules](https://github.com/apolloconfig/apollo/pull/4382)
+* [Fix the delete AppNamespace failed issue](https://github.com/apolloconfig/apollo/pull/4388)
 ------------------
 All issues and pull requests are [here](https://github.com/apolloconfig/apollo/milestone/12?closed=1)
diff --git a/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/AppNamespaceRepository.java b/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/AppNamespaceRepository.java
index 46e783a6a9d..596229d76fc 100644
--- a/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/AppNamespaceRepository.java
+++ b/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/AppNamespaceRepository.java
@@ -43,10 +43,10 @@ public interface AppNamespaceRepository extends PagingAndSortingRepository<AppNa
   List<AppNamespace> findFirst500ByIdGreaterThanOrderByIdAsc(long id);
 
   @Modifying
-  @Query("UPDATE AppNamespace SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE AppId=?1")
+  @Query("UPDATE AppNamespace SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE AppId=?1 and IsDeleted = 0")
   int batchDeleteByAppId(String appId, String operator);
 
   @Modifying
-  @Query("UPDATE AppNamespace SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?3 WHERE AppId=?1 and Name = ?2")
+  @Query("UPDATE AppNamespace SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?3 WHERE AppId=?1 and Name = ?2 and IsDeleted = 0")
   int delete(String appId, String namespaceName, String operator);
 }
diff --git a/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/CommitRepository.java b/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/CommitRepository.java
index dab026c945d..9d5a90bea18 100644
--- a/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/CommitRepository.java
+++ b/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/CommitRepository.java
@@ -35,7 +35,7 @@ List<Commit> findByAppIdAndClusterNameAndNamespaceNameAndDataChangeLastModifiedT
       String appId, String clusterName, String namespaceName, Date dataChangeLastModifiedTime, Pageable pageable);
 
   @Modifying
-  @Query("update Commit set IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?4 where appId=?1 and clusterName=?2 and namespaceName = ?3")
+  @Query("update Commit set IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?4 where appId=?1 and clusterName=?2 and namespaceName = ?3 and IsDeleted = 0")
   int batchDelete(String appId, String clusterName, String namespaceName, String operator);
 
   List<Commit> findByAppIdAndClusterNameAndNamespaceNameAndChangeSetsLikeOrderByIdDesc(String appId, String clusterName, String namespaceName,String changeSets, Pageable page);
diff --git a/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/ItemRepository.java b/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/ItemRepository.java
index d9d61769f4c..136bc269007 100644
--- a/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/ItemRepository.java
+++ b/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/ItemRepository.java
@@ -42,7 +42,7 @@ public interface ItemRepository extends PagingAndSortingRepository<Item, Long> {
   Item findFirst1ByNamespaceIdOrderByLineNumDesc(Long namespaceId);
 
   @Modifying
-  @Query("update Item set IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 where namespaceId = ?1")
+  @Query("update Item set IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 where namespaceId = ?1 and IsDeleted = 0")
   int deleteByNamespaceId(long namespaceId, String operator);
 
 }
diff --git a/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/NamespaceRepository.java b/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/NamespaceRepository.java
index 6ca111c8a97..b0d27810274 100644
--- a/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/NamespaceRepository.java
+++ b/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/NamespaceRepository.java
@@ -33,7 +33,7 @@ public interface NamespaceRepository extends PagingAndSortingRepository<Namespac
   Namespace findByAppIdAndClusterNameAndNamespaceName(String appId, String clusterName, String namespaceName);
 
   @Modifying
-  @Query("update Namespace set IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?3 where appId=?1 and clusterName=?2")
+  @Query("update Namespace set IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?3 where appId=?1 and clusterName=?2 and IsDeleted = 0")
   int batchDelete(String appId, String clusterName, String operator);
 
   List<Namespace> findByAppIdAndNamespaceNameOrderByIdAsc(String appId, String namespaceName);
diff --git a/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/ReleaseHistoryRepository.java b/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/ReleaseHistoryRepository.java
index 1671fa194ef..342dc505c8a 100644
--- a/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/ReleaseHistoryRepository.java
+++ b/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/ReleaseHistoryRepository.java
@@ -39,7 +39,7 @@ Page<ReleaseHistory> findByAppIdAndClusterNameAndNamespaceNameOrderByIdDesc(Stri
   Page<ReleaseHistory> findByReleaseIdAndOperationInOrderByIdDesc(long releaseId, Set<Integer> operations, Pageable pageable);
 
   @Modifying
-  @Query("update ReleaseHistory set IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?4 where appId=?1 and clusterName=?2 and namespaceName = ?3")
+  @Query("update ReleaseHistory set IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?4 where appId=?1 and clusterName=?2 and namespaceName = ?3 and IsDeleted = 0")
   int batchDelete(String appId, String clusterName, String namespaceName, String operator);
 
 }
diff --git a/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/ReleaseRepository.java b/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/ReleaseRepository.java
index ce0afe3ac7f..dfa87b59a8f 100644
--- a/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/ReleaseRepository.java
+++ b/apollo-biz/src/main/java/com/ctrip/framework/apollo/biz/repository/ReleaseRepository.java
@@ -48,7 +48,7 @@ Release findFirstByAppIdAndClusterNameAndNamespaceNameAndIsAbandonedFalseOrderBy
   List<Release> findByIdIn(Set<Long> releaseIds);
 
   @Modifying
-  @Query("update Release set IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?4 where appId=?1 and clusterName=?2 and namespaceName = ?3")
+  @Query("update Release set IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?4 where appId=?1 and clusterName=?2 and namespaceName = ?3 and IsDeleted = 0")
   int batchDelete(String appId, String clusterName, String namespaceName, String operator);
 
   // For release history conversion program, need to delete after conversion it done
diff --git a/apollo-portal/src/main/java/com/ctrip/framework/apollo/openapi/repository/ConsumerRoleRepository.java b/apollo-portal/src/main/java/com/ctrip/framework/apollo/openapi/repository/ConsumerRoleRepository.java
index 7f48c3d16d5..0e9d0b3a31e 100644
--- a/apollo-portal/src/main/java/com/ctrip/framework/apollo/openapi/repository/ConsumerRoleRepository.java
+++ b/apollo-portal/src/main/java/com/ctrip/framework/apollo/openapi/repository/ConsumerRoleRepository.java
@@ -43,6 +43,6 @@ public interface ConsumerRoleRepository extends PagingAndSortingRepository<Consu
   ConsumerRole findByConsumerIdAndRoleId(long consumerId, long roleId);
 
   @Modifying
-  @Query("UPDATE ConsumerRole SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE RoleId in ?1")
+  @Query("UPDATE ConsumerRole SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE RoleId in ?1 and IsDeleted = 0")
   Integer batchDeleteByRoleIds(List<Long> roleIds, String operator);
 }
diff --git a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/AppNamespaceRepository.java b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/AppNamespaceRepository.java
index 8bc7bb0b3ec..0c385915fca 100644
--- a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/AppNamespaceRepository.java
+++ b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/AppNamespaceRepository.java
@@ -35,10 +35,10 @@ public interface AppNamespaceRepository extends PagingAndSortingRepository<AppNa
   List<AppNamespace> findByAppId(String appId);
 
   @Modifying
-  @Query("UPDATE AppNamespace SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy=?2 WHERE AppId=?1")
+  @Query("UPDATE AppNamespace SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy=?2 WHERE AppId=?1 and IsDeleted = 0")
   int batchDeleteByAppId(String appId, String operator);
 
   @Modifying
-  @Query("UPDATE AppNamespace SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?3 WHERE AppId=?1 and Name = ?2")
+  @Query("UPDATE AppNamespace SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?3 WHERE AppId=?1 and Name = ?2 and IsDeleted = 0")
   int delete(String appId, String namespaceName, String operator);
 }
diff --git a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/AppRepository.java b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/AppRepository.java
index 175395e1914..b88bcb3b3bd 100644
--- a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/AppRepository.java
+++ b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/AppRepository.java
@@ -41,6 +41,6 @@ public interface AppRepository extends PagingAndSortingRepository<App, Long> {
   Page<App> findByAppIdContainingOrNameContaining(String appId, String name, Pageable pageable);
 
   @Modifying
-  @Query("UPDATE App SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE AppId=?1")
+  @Query("UPDATE App SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE AppId=?1 and IsDeleted = 0")
   int deleteApp(String appId, String operator);
 }
diff --git a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/FavoriteRepository.java b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/FavoriteRepository.java
index 2198caef21b..37bc92b2f16 100644
--- a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/FavoriteRepository.java
+++ b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/FavoriteRepository.java
@@ -36,6 +36,6 @@ public interface FavoriteRepository extends PagingAndSortingRepository<Favorite,
   Favorite findByUserIdAndAppId(String userId, String appId);
 
   @Modifying
-  @Query("UPDATE Favorite SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE AppId=?1")
+  @Query("UPDATE Favorite SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE AppId=?1 and IsDeleted = 0")
   int batchDeleteByAppId(String appId, String operator);
 }
diff --git a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/PermissionRepository.java b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/PermissionRepository.java
index 476f8cf4400..4fa19e0fa08 100644
--- a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/PermissionRepository.java
+++ b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/PermissionRepository.java
@@ -47,6 +47,6 @@ List<Permission> findByPermissionTypeInAndTargetId(Collection<String> permission
   List<Long> findPermissionIdsByAppIdAndNamespace(String appId, String namespaceName);
 
   @Modifying
-  @Query("UPDATE Permission SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE Id in ?1")
+  @Query("UPDATE Permission SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE Id in ?1 and IsDeleted = 0")
   Integer batchDelete(List<Long> permissionIds, String operator);
 }
diff --git a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/RolePermissionRepository.java b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/RolePermissionRepository.java
index 2b1f0391b14..a23dc3f31ef 100644
--- a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/RolePermissionRepository.java
+++ b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/RolePermissionRepository.java
@@ -36,6 +36,6 @@ public interface RolePermissionRepository extends PagingAndSortingRepository<Rol
   List<RolePermission> findByRoleIdIn(Collection<Long> roleId);
 
   @Modifying
-  @Query("UPDATE RolePermission SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE PermissionId in ?1")
+  @Query("UPDATE RolePermission SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE PermissionId in ?1 and IsDeleted = 0")
   Integer batchDeleteByPermissionIds(List<Long> permissionIds, String operator);
 }
diff --git a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/RoleRepository.java b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/RoleRepository.java
index c7241fd5c85..008cab1559f 100644
--- a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/RoleRepository.java
+++ b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/RoleRepository.java
@@ -43,6 +43,6 @@ public interface RoleRepository extends PagingAndSortingRepository<Role, Long> {
   List<Long> findRoleIdsByAppIdAndNamespace(String appId, String namespaceName);
 
   @Modifying
-  @Query("UPDATE Role SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE Id in ?1")
+  @Query("UPDATE Role SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE Id in ?1 and IsDeleted = 0")
   Integer batchDelete(List<Long> roleIds, String operator);
 }
diff --git a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/UserRoleRepository.java b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/UserRoleRepository.java
index 0796cf045b4..c79893e8979 100644
--- a/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/UserRoleRepository.java
+++ b/apollo-portal/src/main/java/com/ctrip/framework/apollo/portal/repository/UserRoleRepository.java
@@ -45,7 +45,7 @@ public interface UserRoleRepository extends PagingAndSortingRepository<UserRole,
   List<UserRole> findByUserIdInAndRoleId(Collection<String> userId, long roleId);
 
   @Modifying
-  @Query("UPDATE UserRole SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE RoleId in ?1")
+  @Query("UPDATE UserRole SET IsDeleted = 1, DeletedAt = ROUND(UNIX_TIMESTAMP(NOW(4))*1000), DataChange_LastModifiedBy = ?2 WHERE RoleId in ?1 and IsDeleted = 0")
   Integer batchDeleteByRoleIds(List<Long> roleIds, String operator);
 
 }