diff --git a/server/cluster.go b/server/cluster.go
index 649a182882e..572a8008c35 100644
--- a/server/cluster.go
+++ b/server/cluster.go
@@ -539,7 +539,7 @@ func (c *RaftCluster) checkStores() {
 		if store.GetState() != metapb.StoreState_Offline {
 			continue
 		}
-		if cluster.getStoreRegionCount(store.GetId()) == 0 {
+		if c.storeIsEmpty(store.GetId()) {
 			err := c.BuryStore(store.GetId(), false)
 			if err != nil {
 				log.Errorf("bury store %v failed: %v", store, err)
@@ -550,6 +550,25 @@ func (c *RaftCluster) checkStores() {
 	}
 }
 
+func (c *RaftCluster) storeIsEmpty(storeID uint64) bool {
+	cluster := c.cachedCluster
+	if cluster.getStoreRegionCount(storeID) > 0 {
+		return false
+	}
+	// If pd-server is started recently, or becomes leader recently, the check may
+	// happen before any heartbeat from tikv. So we need to check region metas to
+	// verify no region's peer is on the store.
+	regions := cluster.getMetaRegions()
+	for _, region := range regions {
+		for _, p := range region.GetPeers() {
+			if p.GetStoreId() == storeID {
+				return false
+			}
+		}
+	}
+	return true
+}
+
 func (c *RaftCluster) collectMetrics() {
 	cluster := c.cachedCluster