diff --git a/pkg/mock/mockcluster/mockcluster.go b/pkg/mock/mockcluster/mockcluster.go
index 7fe5b3a6a7f3..784a382f97b7 100644
--- a/pkg/mock/mockcluster/mockcluster.go
+++ b/pkg/mock/mockcluster/mockcluster.go
@@ -15,6 +15,7 @@ package mockcluster
 
 import (
 	"fmt"
+	"strconv"
 	"time"
 
 	"github.com/gogo/protobuf/proto"
@@ -583,7 +584,11 @@ func (mc *Cluster) CheckLabelProperty(typ string, labels []*metapb.StoreLabel) b
 
 // PutRegionStores mocks method.
 func (mc *Cluster) PutRegionStores(id uint64, stores ...uint64) {
-	meta := &metapb.Region{Id: id}
+	meta := &metapb.Region{
+		Id:       id,
+		StartKey: []byte(strconv.FormatUint(id, 10)),
+		EndKey:   []byte(strconv.FormatUint(id+1, 10)),
+	}
 	for _, s := range stores {
 		meta.Peers = append(meta.Peers, &metapb.Peer{StoreId: s})
 	}
diff --git a/server/schedulers/balance_region.go b/server/schedulers/balance_region.go
index 08b05b155ca4..ba3cf31b43ae 100644
--- a/server/schedulers/balance_region.go
+++ b/server/schedulers/balance_region.go
@@ -57,6 +57,8 @@ func init() {
 const (
 	// balanceRegionRetryLimit is the limit to retry schedule for selected store.
 	balanceRegionRetryLimit = 10
+	// BalanceEmptyRegionThreshold is a threshold which allow balance the empty region if the region number is less than this threshold.
+	balanceEmptyRegionThreshold = 50
 	// BalanceRegionName is balance region scheduler name.
 	BalanceRegionName = "balance-region-scheduler"
 	// BalanceRegionType is balance region scheduler type.
@@ -142,6 +144,7 @@ func (s *balanceRegionScheduler) Schedule(cluster opt.Cluster) []*operator.Opera
 		return stores[i].RegionScore(opts.GetRegionScoreFormulaVersion(), opts.GetHighSpaceRatio(), opts.GetLowSpaceRatio(), iOp, -1) >
 			stores[j].RegionScore(opts.GetRegionScoreFormulaVersion(), opts.GetHighSpaceRatio(), opts.GetLowSpaceRatio(), jOp, -1)
 	})
+	regionCount := cluster.GetRegionCount()
 	for _, source := range stores {
 		sourceID := source.GetID()
 
@@ -168,7 +171,7 @@ func (s *balanceRegionScheduler) Schedule(cluster opt.Cluster) []*operator.Opera
 			log.Debug("select region", zap.String("scheduler", s.GetName()), zap.Uint64("region-id", region.GetID()))
 
 			// Skip the empty region
-			if region.GetApproximateSize() <= core.EmptyRegionApproximateSize {
+			if region.GetApproximateSize() <= core.EmptyRegionApproximateSize && regionCount > balanceEmptyRegionThreshold {
 				log.Debug("region is empty", zap.String("scheduler", s.GetName()), zap.Uint64("region-id", region.GetID()))
 				schedulerCounter.WithLabelValues(s.GetName(), "empty-region").Inc()
 				continue
diff --git a/server/schedulers/balance_test.go b/server/schedulers/balance_test.go
index 49eebc0e2822..509599807608 100644
--- a/server/schedulers/balance_test.go
+++ b/server/schedulers/balance_test.go
@@ -960,6 +960,12 @@ func (s *testBalanceRegionSchedulerSuite) TestEmptyRegion(c *C) {
 	)
 	tc.PutRegion(region)
 	operators := sb.Schedule(tc)
+	c.Assert(operators, NotNil)
+
+	for i := uint64(10); i < 60; i++ {
+		tc.PutRegionStores(i, 1, 3, 4)
+	}
+	operators = sb.Schedule(tc)
 	c.Assert(operators, IsNil)
 }