diff --git a/pkg/core/region.go b/pkg/core/region.go
index 8d0379f266f..6631005a608 100644
--- a/pkg/core/region.go
+++ b/pkg/core/region.go
@@ -73,8 +73,26 @@ type RegionInfo struct {
 	queryStats        *pdpb.QueryStats
 	flowRoundDivisor  uint64
 	// buckets is not thread unsafe, it should be accessed by the request `report buckets` with greater version.
-	buckets       unsafe.Pointer
-	fromHeartbeat bool
+	buckets unsafe.Pointer
+	// source is used to indicate region's source, such as Storage/Sync/Heartbeat.
+	source RegionSource
+}
+
+// RegionSource is the source of region.
+type RegionSource uint32
+
+const (
+	// Storage means this region's meta info might be stale.
+	Storage RegionSource = iota
+	// Sync means this region's meta info is relatively fresher.
+	Sync
+	// Heartbeat means this region's meta info is relatively fresher.
+	Heartbeat
+)
+
+// LoadedFromStorage means this region's meta info loaded from storage.
+func (r *RegionInfo) LoadedFromStorage() bool {
+	return r.source == Storage
 }
 
 // NewRegionInfo creates RegionInfo with region's meta and leader peer.
@@ -192,6 +210,7 @@ func RegionFromHeartbeat(heartbeat RegionHeartbeatRequest, opts ...RegionCreateO
 		approximateKeys: int64(heartbeat.GetApproximateKeys()),
 		interval:        heartbeat.GetInterval(),
 		queryStats:      heartbeat.GetQueryStats(),
+		source:          Heartbeat,
 	}
 
 	// scheduling service doesn't need the following fields.
@@ -667,11 +686,6 @@ func (r *RegionInfo) IsFlashbackChanged(l *RegionInfo) bool {
 	return r.meta.FlashbackStartTs != l.meta.FlashbackStartTs || r.meta.IsInFlashback != l.meta.IsInFlashback
 }
 
-// IsFromHeartbeat returns whether the region info is from the region heartbeat.
-func (r *RegionInfo) IsFromHeartbeat() bool {
-	return r.fromHeartbeat
-}
-
 func (r *RegionInfo) isInvolved(startKey, endKey []byte) bool {
 	return bytes.Compare(r.GetStartKey(), startKey) >= 0 && (len(endKey) == 0 || (len(r.GetEndKey()) > 0 && bytes.Compare(r.GetEndKey(), endKey) <= 0))
 }
@@ -711,7 +725,7 @@ func GenerateRegionGuideFunc(enableLog bool) RegionGuideFunc {
 			}
 			saveKV, saveCache, isNew = true, true, true
 		} else {
-			if !origin.IsFromHeartbeat() {
+			if origin.LoadedFromStorage() {
 				isNew = true
 			}
 			r := region.GetRegionEpoch()
@@ -1323,6 +1337,13 @@ func (r *RegionsInfo) GetStoreWriteRate(storeID uint64) (bytesRate, keysRate flo
 	return
 }
 
+// GetClusterNotFromStorageRegionsCnt gets the total count of regions that not loaded from storage anymore
+func (r *RegionsInfo) GetClusterNotFromStorageRegionsCnt() int {
+	r.st.RLock()
+	defer r.st.RUnlock()
+	return r.tree.notFromStorageRegionsCnt
+}
+
 // GetMetaRegions gets a set of metapb.Region from regionMap
 func (r *RegionsInfo) GetMetaRegions() []*metapb.Region {
 	r.t.RLock()
diff --git a/pkg/core/region_option.go b/pkg/core/region_option.go
index ce959905810..36db7cf3460 100644
--- a/pkg/core/region_option.go
+++ b/pkg/core/region_option.go
@@ -381,10 +381,10 @@ func WithInterval(interval *pdpb.TimeInterval) RegionCreateOption {
 	}
 }
 
-// SetFromHeartbeat sets if the region info comes from the region heartbeat.
-func SetFromHeartbeat(fromHeartbeat bool) RegionCreateOption {
+// SetSource sets the region info's come from.
+func SetSource(source RegionSource) RegionCreateOption {
 	return func(region *RegionInfo) {
-		region.fromHeartbeat = fromHeartbeat
+		region.source = source
 	}
 }
 
diff --git a/pkg/core/region_tree.go b/pkg/core/region_tree.go
index db1c8c28fc7..ed3445de6b6 100644
--- a/pkg/core/region_tree.go
+++ b/pkg/core/region_tree.go
@@ -61,14 +61,17 @@ type regionTree struct {
 	totalSize           int64
 	totalWriteBytesRate float64
 	totalWriteKeysRate  float64
+	// count the number of regions that not loaded from storage.
+	notFromStorageRegionsCnt int
 }
 
 func newRegionTree() *regionTree {
 	return &regionTree{
-		tree:                btree.NewG[*regionItem](defaultBTreeDegree),
-		totalSize:           0,
-		totalWriteBytesRate: 0,
-		totalWriteKeysRate:  0,
+		tree:                     btree.NewG[*regionItem](defaultBTreeDegree),
+		totalSize:                0,
+		totalWriteBytesRate:      0,
+		totalWriteKeysRate:       0,
+		notFromStorageRegionsCnt: 0,
 	}
 }
 
@@ -112,6 +115,9 @@ func (t *regionTree) update(item *regionItem, withOverlaps bool, overlaps ...*re
 	regionWriteBytesRate, regionWriteKeysRate := region.GetWriteRate()
 	t.totalWriteBytesRate += regionWriteBytesRate
 	t.totalWriteKeysRate += regionWriteKeysRate
+	if !region.LoadedFromStorage() {
+		t.notFromStorageRegionsCnt++
+	}
 
 	if !withOverlaps {
 		overlaps = t.overlaps(item)
@@ -133,6 +139,9 @@ func (t *regionTree) update(item *regionItem, withOverlaps bool, overlaps ...*re
 		regionWriteBytesRate, regionWriteKeysRate = old.GetWriteRate()
 		t.totalWriteBytesRate -= regionWriteBytesRate
 		t.totalWriteKeysRate -= regionWriteKeysRate
+		if !old.LoadedFromStorage() {
+			t.notFromStorageRegionsCnt--
+		}
 	}
 
 	return result
@@ -149,6 +158,15 @@ func (t *regionTree) updateStat(origin *RegionInfo, region *RegionInfo) {
 	regionWriteBytesRate, regionWriteKeysRate = origin.GetWriteRate()
 	t.totalWriteBytesRate -= regionWriteBytesRate
 	t.totalWriteKeysRate -= regionWriteKeysRate
+
+	// If the region meta information not loaded from storage anymore, decrease the counter.
+	if origin.LoadedFromStorage() && !region.LoadedFromStorage() {
+		t.notFromStorageRegionsCnt++
+	}
+	// If the region meta information updated to load from storage, increase the counter.
+	if !origin.LoadedFromStorage() && region.LoadedFromStorage() {
+		t.notFromStorageRegionsCnt--
+	}
 }
 
 // remove removes a region if the region is in the tree.
@@ -168,6 +186,9 @@ func (t *regionTree) remove(region *RegionInfo) {
 	regionWriteBytesRate, regionWriteKeysRate := result.GetWriteRate()
 	t.totalWriteBytesRate -= regionWriteBytesRate
 	t.totalWriteKeysRate -= regionWriteKeysRate
+	if !region.LoadedFromStorage() {
+		t.notFromStorageRegionsCnt--
+	}
 	t.tree.Delete(item)
 }
 
diff --git a/pkg/mcs/scheduling/server/cluster.go b/pkg/mcs/scheduling/server/cluster.go
index e8489fdaa15..891a645053f 100644
--- a/pkg/mcs/scheduling/server/cluster.go
+++ b/pkg/mcs/scheduling/server/cluster.go
@@ -547,7 +547,7 @@ func (c *Cluster) processRegionHeartbeat(region *core.RegionInfo) error {
 		// To prevent a concurrent heartbeat of another region from overriding the up-to-date region info by a stale one,
 		// check its validation again here.
 		//
-		// However it can't solve the race condition of concurrent heartbeats from the same region.
+		// However, it can't solve the race condition of concurrent heartbeats from the same region.
 		if overlaps, err = c.AtomicCheckAndPutRegion(region); err != nil {
 			return err
 		}
diff --git a/pkg/mcs/scheduling/server/grpc_service.go b/pkg/mcs/scheduling/server/grpc_service.go
index 4558688822a..b9b682dfa74 100644
--- a/pkg/mcs/scheduling/server/grpc_service.go
+++ b/pkg/mcs/scheduling/server/grpc_service.go
@@ -161,7 +161,7 @@ func (s *Service) RegionHeartbeat(stream schedulingpb.Scheduling_RegionHeartbeat
 			s.hbStreams.BindStream(storeID, server)
 			lastBind = time.Now()
 		}
-		region := core.RegionFromHeartbeat(request, core.SetFromHeartbeat(true))
+		region := core.RegionFromHeartbeat(request, core.SetSource(core.Heartbeat))
 		err = c.HandleRegionHeartbeat(region)
 		if err != nil {
 			// TODO: if we need to send the error back to API server.
diff --git a/pkg/schedule/prepare_checker.go b/pkg/schedule/prepare_checker.go
index cd4b076b2d6..c7faa57af81 100644
--- a/pkg/schedule/prepare_checker.go
+++ b/pkg/schedule/prepare_checker.go
@@ -17,8 +17,10 @@ package schedule
 import (
 	"time"
 
+	"github.com/pingcap/log"
 	"github.com/tikv/pd/pkg/core"
 	"github.com/tikv/pd/pkg/utils/syncutil"
+	"go.uber.org/zap"
 )
 
 type prepareChecker struct {
@@ -47,8 +49,15 @@ func (checker *prepareChecker) check(c *core.BasicCluster) bool {
 		checker.prepared = true
 		return true
 	}
+	notLoadedFromRegionsCnt := c.GetClusterNotFromStorageRegionsCnt()
+	totalRegionsCnt := c.GetTotalRegionCount()
+	if float64(notLoadedFromRegionsCnt) > float64(totalRegionsCnt)*collectFactor {
+		log.Info("meta not loaded from region number is satisfied, finish prepare checker", zap.Int("not-from-storage-region", notLoadedFromRegionsCnt), zap.Int("total-region", totalRegionsCnt))
+		checker.prepared = true
+		return true
+	}
 	// The number of active regions should be more than total region of all stores * collectFactor
-	if float64(c.GetTotalRegionCount())*collectFactor > float64(checker.sum) {
+	if float64(totalRegionsCnt)*collectFactor > float64(checker.sum) {
 		return false
 	}
 	for _, store := range c.GetStores() {
diff --git a/pkg/storage/endpoint/meta.go b/pkg/storage/endpoint/meta.go
index 4ba9eb42c5c..d83e2b386c8 100644
--- a/pkg/storage/endpoint/meta.go
+++ b/pkg/storage/endpoint/meta.go
@@ -203,7 +203,7 @@ func (se *StorageEndpoint) LoadRegions(ctx context.Context, f func(region *core.
 			}
 
 			nextID = region.GetId() + 1
-			overlaps := f(core.NewRegionInfo(region, nil))
+			overlaps := f(core.NewRegionInfo(region, nil, core.SetSource(core.Storage)))
 			for _, item := range overlaps {
 				if err := se.DeleteRegion(item.GetMeta()); err != nil {
 					return err
diff --git a/pkg/storage/storage_test.go b/pkg/storage/storage_test.go
index 77f94183403..dbb5a03b264 100644
--- a/pkg/storage/storage_test.go
+++ b/pkg/storage/storage_test.go
@@ -407,6 +407,7 @@ func saveRegions(lb *levelDBBackend, n int, ratio int) error {
 }
 
 func benchmarkLoadRegions(b *testing.B, n int, ratio int) {
+	re := require.New(b)
 	ctx := context.Background()
 	dir := b.TempDir()
 	lb, err := newLevelDBBackend(ctx, dir, nil)
@@ -426,10 +427,8 @@ func benchmarkLoadRegions(b *testing.B, n int, ratio int) {
 	}()
 
 	b.ResetTimer()
-	err = lb.LoadRegions(ctx, cluster.CheckAndPutRegion)
-	if err != nil {
-		b.Fatal(err)
-	}
+	err = lb.LoadRegions(context.Background(), cluster.CheckAndPutRegion)
+	re.NoError(err)
 }
 
 var volumes = []struct {
diff --git a/pkg/syncer/client.go b/pkg/syncer/client.go
index ac409f90115..f61ce320a74 100644
--- a/pkg/syncer/client.go
+++ b/pkg/syncer/client.go
@@ -95,7 +95,7 @@ func (s *RegionSyncer) StartSyncWithLeader(addr string) {
 		log.Info("region syncer start load region")
 		start := time.Now()
 		err := storage.TryLoadRegionsOnce(ctx, regionStorage, bc.CheckAndPutRegion)
-		log.Info("region syncer finished load region", zap.Duration("time-cost", time.Since(start)))
+		log.Info("region syncer finished load regions", zap.Duration("time-cost", time.Since(start)))
 		if err != nil {
 			log.Warn("failed to load regions", errs.ZapError(err))
 		}
@@ -183,10 +183,10 @@ func (s *RegionSyncer) StartSyncWithLeader(addr string) {
 							core.SetWrittenKeys(stats[i].KeysWritten),
 							core.SetReadBytes(stats[i].BytesRead),
 							core.SetReadKeys(stats[i].KeysRead),
-							core.SetFromHeartbeat(false),
+							core.SetSource(core.Sync),
 						)
 					} else {
-						region = core.NewRegionInfo(r, regionLeader, core.SetFromHeartbeat(false))
+						region = core.NewRegionInfo(r, regionLeader, core.SetSource(core.Sync))
 					}
 
 					origin, _, err := bc.PreCheckPutRegion(region)
diff --git a/server/cluster/cluster.go b/server/cluster/cluster.go
index 332a8b27a3f..094dd482107 100644
--- a/server/cluster/cluster.go
+++ b/server/cluster/cluster.go
@@ -593,7 +593,7 @@ func (c *RaftCluster) LoadClusterInfo() (*RaftCluster, error) {
 	start = time.Now()
 
 	// used to load region from kv storage to cache storage.
-	if err := storage.TryLoadRegionsOnce(c.ctx, c.storage, c.core.CheckAndPutRegion); err != nil {
+	if err = storage.TryLoadRegionsOnce(c.ctx, c.storage, c.core.CheckAndPutRegion); err != nil {
 		return nil, err
 	}
 	log.Info("load regions",
diff --git a/server/cluster/cluster_test.go b/server/cluster/cluster_test.go
index 31f6bb357c3..b7b9dcfb736 100644
--- a/server/cluster/cluster_test.go
+++ b/server/cluster/cluster_test.go
@@ -1002,7 +1002,7 @@ func TestRegionSizeChanged(t *testing.T) {
 		core.WithLeader(region.GetPeers()[2]),
 		core.SetApproximateSize(curMaxMergeSize-1),
 		core.SetApproximateKeys(curMaxMergeKeys-1),
-		core.SetFromHeartbeat(true),
+		core.SetSource(core.Heartbeat),
 	)
 	cluster.processRegionHeartbeat(region)
 	regionID := region.GetID()
@@ -1012,7 +1012,7 @@ func TestRegionSizeChanged(t *testing.T) {
 		core.WithLeader(region.GetPeers()[2]),
 		core.SetApproximateSize(curMaxMergeSize+1),
 		core.SetApproximateKeys(curMaxMergeKeys+1),
-		core.SetFromHeartbeat(true),
+		core.SetSource(core.Heartbeat),
 	)
 	cluster.processRegionHeartbeat(region)
 	re.False(cluster.regionStats.IsRegionStatsType(regionID, statistics.UndersizedRegion))
diff --git a/server/grpc_service.go b/server/grpc_service.go
index febb666c22d..d9f37a64d7d 100644
--- a/server/grpc_service.go
+++ b/server/grpc_service.go
@@ -1316,7 +1316,7 @@ func (s *GrpcServer) RegionHeartbeat(stream pdpb.PD_RegionHeartbeatServer) error
 			lastBind = time.Now()
 		}
 
-		region := core.RegionFromHeartbeat(request, flowRoundOption, core.SetFromHeartbeat(true))
+		region := core.RegionFromHeartbeat(request, flowRoundOption)
 		if region.GetLeader() == nil {
 			log.Error("invalid request, the leader is nil", zap.Reflect("request", request), errs.ZapError(errs.ErrLeaderNil))
 			regionHeartbeatCounter.WithLabelValues(storeAddress, storeLabel, "report", "invalid-leader").Inc()
diff --git a/tests/server/region_syncer/region_syncer_test.go b/tests/server/region_syncer/region_syncer_test.go
index f672f82f1f6..b73d4abb9b5 100644
--- a/tests/server/region_syncer/region_syncer_test.go
+++ b/tests/server/region_syncer/region_syncer_test.go
@@ -246,6 +246,52 @@ func TestPrepareChecker(t *testing.T) {
 	re.NoError(failpoint.Disable("github.com/tikv/pd/pkg/schedule/changeCoordinatorTicker"))
 }
 
+// ref: https://github.com/tikv/pd/issues/6988
+func TestPrepareCheckerWithTransferLeader(t *testing.T) {
+	re := require.New(t)
+	ctx, cancel := context.WithCancel(context.Background())
+	defer cancel()
+	re.NoError(failpoint.Enable("github.com/tikv/pd/pkg/schedule/changeCoordinatorTicker", `return(true)`))
+	cluster, err := tests.NewTestCluster(ctx, 1, func(conf *config.Config, serverName string) { conf.PDServerCfg.UseRegionStorage = true })
+	defer cluster.Destroy()
+	re.NoError(err)
+
+	err = cluster.RunInitialServers()
+	re.NoError(err)
+	cluster.WaitLeader()
+	leaderServer := cluster.GetServer(cluster.GetLeader())
+	re.NoError(leaderServer.BootstrapCluster())
+	rc := leaderServer.GetServer().GetRaftCluster()
+	re.NotNil(rc)
+	regionLen := 100
+	regions := initRegions(regionLen)
+	for _, region := range regions {
+		err = rc.HandleRegionHeartbeat(region)
+		re.NoError(err)
+	}
+	// ensure flush to region storage
+	time.Sleep(3 * time.Second)
+	re.True(leaderServer.GetRaftCluster().IsPrepared())
+
+	// join new PD
+	pd2, err := cluster.Join(ctx)
+	re.NoError(err)
+	err = pd2.Run()
+	re.NoError(err)
+	// waiting for synchronization to complete
+	time.Sleep(3 * time.Second)
+	err = cluster.ResignLeader()
+	re.NoError(err)
+	re.Equal("pd2", cluster.WaitLeader())
+
+	// transfer leader to pd1, can start coordinator immediately.
+	err = cluster.ResignLeader()
+	re.NoError(err)
+	re.Equal("pd1", cluster.WaitLeader())
+	re.True(rc.IsPrepared())
+	re.NoError(failpoint.Disable("github.com/tikv/pd/pkg/schedule/changeCoordinatorTicker"))
+}
+
 func initRegions(regionLen int) []*core.RegionInfo {
 	allocator := &idAllocator{allocator: mockid.NewIDAllocator()}
 	regions := make([]*core.RegionInfo, 0, regionLen)
@@ -264,7 +310,7 @@ func initRegions(regionLen int) []*core.RegionInfo {
 				{Id: allocator.alloc(), StoreId: uint64(3)},
 			},
 		}
-		region := core.NewRegionInfo(r, r.Peers[0])
+		region := core.NewRegionInfo(r, r.Peers[0], core.SetSource(core.Heartbeat))
 		// Here is used to simulate the upgrade process.
 		if i < regionLen/2 {
 			buckets := &metapb.Buckets{