diff --git a/server/cluster/cluster.go b/server/cluster/cluster.go
index 3d4eef97ef3..8b14345fcf2 100644
--- a/server/cluster/cluster.go
+++ b/server/cluster/cluster.go
@@ -51,11 +51,6 @@ const (
 	defaultChangedRegionsLimit = 10000
 )
 
-// ErrRegionIsStale is error info for region is stale.
-var ErrRegionIsStale = func(region *metapb.Region, origin *metapb.Region) error {
-	return errors.Errorf("region is stale: region %v origin %v", region, origin)
-}
-
 // Server is the interface for cluster.
 type Server interface {
 	GetAllocator() *id.AllocatorImpl
@@ -242,7 +237,17 @@ func (c *RaftCluster) LoadClusterInfo() (*RaftCluster, error) {
 
 	start = time.Now()
 
-	if err := c.storage.LoadRegions(c.core.PutRegion); err != nil {
+	// used to load region from kv storage to cache storage.
+	putRegion := func(region *core.RegionInfo) []*core.RegionInfo {
+		origin, err := c.core.PreCheckPutRegion(region)
+		if err != nil {
+			log.Warn("region is stale", zap.Error(err), zap.Stringer("origin", origin.GetMeta()))
+			// return the state region to delete.
+			return []*core.RegionInfo{region}
+		}
+		return c.core.PutRegion(region)
+	}
+	if err := c.storage.LoadRegions(putRegion); err != nil {
 		return nil, err
 	}
 	log.Info("load regions",
@@ -394,14 +399,10 @@ func (c *RaftCluster) HandleStoreHeartbeat(stats *pdpb.StoreStats) error {
 // processRegionHeartbeat updates the region information.
 func (c *RaftCluster) processRegionHeartbeat(region *core.RegionInfo) error {
 	c.RLock()
-	origin := c.GetRegion(region.GetID())
-	if origin == nil {
-		for _, item := range c.core.GetOverlaps(region) {
-			if region.GetRegionEpoch().GetVersion() < item.GetRegionEpoch().GetVersion() {
-				c.RUnlock()
-				return ErrRegionIsStale(region.GetMeta(), item.GetMeta())
-			}
-		}
+	origin, err := c.core.PreCheckPutRegion(region)
+	if err != nil {
+		c.RUnlock()
+		return err
 	}
 	writeItems := c.CheckWriteStatus(region)
 	readItems := c.CheckReadStatus(region)
@@ -420,10 +421,6 @@ func (c *RaftCluster) processRegionHeartbeat(region *core.RegionInfo) error {
 	} else {
 		r := region.GetRegionEpoch()
 		o := origin.GetRegionEpoch()
-		// Region meta is stale, return an error.
-		if r.GetVersion() < o.GetVersion() || r.GetConfVer() < o.GetConfVer() {
-			return ErrRegionIsStale(region.GetMeta(), origin.GetMeta())
-		}
 		if r.GetVersion() > o.GetVersion() {
 			log.Info("region Version changed",
 				zap.Uint64("region-id", region.GetID()),
@@ -1454,6 +1451,8 @@ func (c *RaftCluster) CheckReadStatus(region *core.RegionInfo) []*statistics.Hot
 	return c.hotSpotCache.CheckRead(region, c.storesStats)
 }
 
+// TODO: remove me.
+// only used in test.
 func (c *RaftCluster) putRegion(region *core.RegionInfo) error {
 	c.Lock()
 	defer c.Unlock()
diff --git a/server/cluster/cluster_test.go b/server/cluster/cluster_test.go
index b000937a6bd..ef33c14165b 100644
--- a/server/cluster/cluster_test.go
+++ b/server/cluster/cluster_test.go
@@ -758,7 +758,7 @@ func checkStaleRegion(origin *metapb.Region, region *metapb.Region) error {
 	e := region.GetRegionEpoch()
 
 	if e.GetVersion() < o.GetVersion() || e.GetConfVer() < o.GetConfVer() {
-		return ErrRegionIsStale(region, origin)
+		return core.ErrRegionIsStale(region, origin)
 	}
 
 	return nil
diff --git a/server/core/basic_cluster.go b/server/core/basic_cluster.go
index 3730ff5b85c..b53c403127c 100644
--- a/server/core/basic_cluster.go
+++ b/server/core/basic_cluster.go
@@ -282,6 +282,29 @@ func (bc *BasicCluster) TakeStore(storeID uint64) *StoreInfo {
 	return bc.Stores.TakeStore(storeID)
 }
 
+// PreCheckPutRegion checks if the region is valid to put.
+func (bc *BasicCluster) PreCheckPutRegion(region *RegionInfo) (*RegionInfo, error) {
+	bc.RLock()
+	for _, item := range bc.Regions.GetOverlaps(region) {
+		if region.GetRegionEpoch().GetVersion() < item.GetRegionEpoch().GetVersion() {
+			bc.RUnlock()
+			return nil, ErrRegionIsStale(region.GetMeta(), item.GetMeta())
+		}
+	}
+	origin := bc.Regions.GetRegion(region.GetID())
+	bc.RUnlock()
+	if origin == nil {
+		return nil, nil
+	}
+	r := region.GetRegionEpoch()
+	o := origin.GetRegionEpoch()
+	// Region meta is stale, return an error.
+	if r.GetVersion() < o.GetVersion() || r.GetConfVer() < o.GetConfVer() {
+		return origin, ErrRegionIsStale(region.GetMeta(), origin.GetMeta())
+	}
+	return origin, nil
+}
+
 // PutRegion put a region.
 func (bc *BasicCluster) PutRegion(region *RegionInfo) []*RegionInfo {
 	bc.Lock()
diff --git a/server/core/errors.go b/server/core/errors.go
index a58b9adcc53..5d0e0ea48b6 100644
--- a/server/core/errors.go
+++ b/server/core/errors.go
@@ -21,6 +21,8 @@ import (
 	"net/http"
 
 	"github.com/pingcap/errcode"
+	"github.com/pingcap/kvproto/pkg/metapb"
+	"github.com/pkg/errors"
 )
 
 var (
@@ -61,3 +63,8 @@ func (e StoreBlockedErr) Error() string {
 
 // Code returns StoreBlockedCode
 func (e StoreBlockedErr) Code() errcode.Code { return StoreBlockedCode }
+
+// ErrRegionIsStale is error info for region is stale.
+var ErrRegionIsStale = func(region *metapb.Region, origin *metapb.Region) error {
+	return errors.Errorf("region is stale: region %v origin %v", region, origin)
+}
diff --git a/server/core/region.go b/server/core/region.go
index ad83611d43f..f30bf0a3b79 100644
--- a/server/core/region.go
+++ b/server/core/region.go
@@ -304,6 +304,9 @@ func (r *RegionInfo) GetID() uint64 {
 
 // GetMeta returns the meta information of the region.
 func (r *RegionInfo) GetMeta() *metapb.Region {
+	if r == nil {
+		return nil
+	}
 	return r.meta
 }
 
diff --git a/tests/server/region_syncer/region_syncer_test.go b/tests/server/region_syncer/region_syncer_test.go
index 45f3044fc35..9588deb2ed5 100644
--- a/tests/server/region_syncer/region_syncer_test.go
+++ b/tests/server/region_syncer/region_syncer_test.go
@@ -94,6 +94,29 @@ func (s *serverTestSuite) TestRegionSyncer(c *C) {
 		err = rc.HandleRegionHeartbeat(region)
 		c.Assert(err, IsNil)
 	}
+	// merge case
+	// region2 -> region1 -> region0
+	// merge A to B will increases version to max(versionA, versionB)+1, but does not increase conver
+	regions[0] = regions[0].Clone(core.WithEndKey(regions[2].GetEndKey()), core.WithIncVersion(), core.WithIncVersion())
+	err = rc.HandleRegionHeartbeat(regions[2])
+	c.Assert(err, IsNil)
+
+	// merge case
+	// region3 -> region4
+	// merge A to B will increases version to max(versionA, versionB)+1, but does not increase conver
+	regions[4] = regions[3].Clone(core.WithEndKey(regions[4].GetEndKey()), core.WithIncVersion())
+	err = rc.HandleRegionHeartbeat(regions[4])
+	c.Assert(err, IsNil)
+
+	// merge case
+	// region0 -> region4
+	// merge A to B will increases version to max(versionA, versionB)+1, but does not increase conver
+	regions[4] = regions[0].Clone(core.WithEndKey(regions[4].GetEndKey()), core.WithIncVersion(), core.WithIncVersion())
+	err = rc.HandleRegionHeartbeat(regions[4])
+	c.Assert(err, IsNil)
+	regions = regions[4:]
+	regionLen = len(regions)
+
 	// ensure flush to region storage, we use a duration larger than the
 	// region storage flush rate limit (3s).
 	time.Sleep(4 * time.Second)
@@ -104,6 +127,9 @@ func (s *serverTestSuite) TestRegionSyncer(c *C) {
 	c.Assert(leaderServer, NotNil)
 	loadRegions := leaderServer.GetServer().GetRaftCluster().GetRegions()
 	c.Assert(len(loadRegions), Equals, regionLen)
+	for _, region := range regions {
+		c.Assert(leaderServer.GetRegionInfoByID(region.GetID()).GetMeta(), DeepEquals, region.GetMeta())
+	}
 }
 
 func (s *serverTestSuite) TestFullSyncWithAddMember(c *C) {