diff --git a/pkg/core/region.go b/pkg/core/region.go
index be8fcddc179..affe6e14406 100644
--- a/pkg/core/region.go
+++ b/pkg/core/region.go
@@ -1041,10 +1041,10 @@ func (r *RegionsInfo) CheckAndPutRootTree(ctx *MetaProcessContext, region *Regio
 // Usually used with CheckAndPutRootTree together.
 func (r *RegionsInfo) CheckAndPutSubTree(region *RegionInfo) {
 	// new region get from root tree again
-	var newRegion *RegionInfo
-	newRegion = r.GetRegion(region.GetID())
+	newRegion := r.GetRegion(region.GetID())
 	if newRegion == nil {
-		newRegion = region
+		// Make sure there is this region in the root tree, so as to ensure the correctness of reference count
+		return
 	}
 	r.UpdateSubTreeOrderInsensitive(newRegion)
 }
diff --git a/pkg/core/region_test.go b/pkg/core/region_test.go
index 43629fccda0..4a418a16ebc 100644
--- a/pkg/core/region_test.go
+++ b/pkg/core/region_test.go
@@ -1021,3 +1021,12 @@ func TestUpdateRegionEventualConsistency(t *testing.T) {
 		re.Equal(int32(2), item.GetRef())
 	}
 }
+
+func TestCheckAndPutSubTree(t *testing.T) {
+	re := require.New(t)
+	regions := NewRegionsInfo()
+	region := NewTestRegionInfo(1, 1, []byte("a"), []byte("b"))
+	regions.CheckAndPutSubTree(region)
+	// should failed to put because the root tree is missing
+	re.Equal(0, regions.tree.length())
+}