diff --git a/session/bootstrap.go b/session/bootstrap.go
index 21742acd1..cb888632a 100644
--- a/session/bootstrap.go
+++ b/session/bootstrap.go
@@ -449,7 +449,7 @@ func bootstrap(s Session) {
 		if dom.DDL().OwnerManager().IsOwner() {
 			doDDLWorks(s)
 			doDMLWorks(s)
-			doBootstrapSQLFile(s)
+			runBootstrapSQLFile = true
 			logutil.BgLogger().Info("bootstrap successful",
 				zap.Duration("take time", time.Since(startTime)))
 			return
@@ -638,6 +638,9 @@ var currentBootstrapVersion int64 = version93
 // DDL owner key's expired time is ManagerSessionTTL seconds, we should wait the time and give more time to have a chance to finish it.
 var internalSQLTimeout = owner.ManagerSessionTTL + 15
 
+// whether to run the sql file in bootstrap.
+var runBootstrapSQLFile = false
+
 var (
 	bootstrapVersion = []func(Session, int64){
 		upgradeToVer2,
@@ -2020,6 +2023,7 @@ func doDDLWorks(s Session) {
 // It is useful for setting the initial value of GLOBAL variables.
 func doBootstrapSQLFile(s Session) {
 	sqlFile := config.GetGlobalConfig().InitializeSQLFile
+	ctx := kv.WithInternalSourceType(context.Background(), kv.InternalTxnBootstrap)
 	if sqlFile == "" {
 		return
 	}
@@ -2033,7 +2037,7 @@ func doBootstrapSQLFile(s Session) {
 		logutil.BgLogger().Fatal("unable to parse InitializeSQLFile", zap.Error(err))
 	}
 	for _, stmt := range stmts {
-		rs, err := s.ExecuteStmt(context.Background(), stmt)
+		rs, err := s.ExecuteStmt(ctx, stmt)
 		if err != nil {
 			logutil.BgLogger().Warn("InitializeSQLFile error", zap.Error(err))
 		}
diff --git a/session/session.go b/session/session.go
index c8895ea3b..61a25a8bf 100644
--- a/session/session.go
+++ b/session/session.go
@@ -2733,7 +2733,7 @@ func BootstrapSession(store kv.Storage) (*domain.Domain, error) {
 	}
 
 	concurrency := int(config.GetGlobalConfig().Performance.StatsLoadConcurrency)
-	ses, err := createSessions(store, 7+concurrency)
+	ses, err := createSessions(store, 8+concurrency)
 	if err != nil {
 		return nil, err
 	}
@@ -2803,11 +2803,19 @@ func BootstrapSession(store kv.Storage) (*domain.Domain, error) {
 		}()
 	}
 
+	if runBootstrapSQLFile {
+		pm := &privileges.UserPrivileges{
+			Handle: dom.PrivilegeHandle(),
+		}
+		privilege.BindPrivilegeManager(ses[6], pm)
+		doBootstrapSQLFile(ses[6])
+	}
+
 	// A sub context for update table stats, and other contexts for concurrent stats loading.
 	cnt := 1 + concurrency
 	subCtxs := make([]sessionctx.Context, cnt)
 	for i := 0; i < cnt; i++ {
-		subCtxs[i] = sessionctx.Context(ses[6+i])
+		subCtxs[i] = sessionctx.Context(ses[7+i])
 	}
 	if err = dom.LoadAndUpdateStatsLoop(subCtxs); err != nil {
 		return nil, err