diff --git a/session/bootstrap.go b/session/bootstrap.go
index 67b1a285c07a7..b32e7de3b4be8 100644
--- a/session/bootstrap.go
+++ b/session/bootstrap.go
@@ -384,6 +384,8 @@ const (
 	version44 = 44
 	// version45 introduces CONFIG_PRIV for SET CONFIG statements.
 	version45 = 45
+	// version46 fix a bug in v3.1.1.
+	version46 = 46
 )
 
 var (
@@ -432,6 +434,7 @@ var (
 		upgradeToVer43,
 		upgradeToVer44,
 		upgradeToVer45,
+		upgradeToVer46,
 	}
 )
 
@@ -1045,6 +1048,18 @@ func upgradeToVer45(s Session, ver int64) {
 	mustExecute(s, "UPDATE HIGH_PRIORITY mysql.user SET Config_priv='Y' where Super_priv='Y'")
 }
 
+// In v3.1.1, we wrongly replace the context of upgradeToVer39 with upgradeToVer44. If we upgrade from v3.1.1 to a newer version,
+// upgradeToVer39 will be missed. So we redo upgradeToVer39 here to make sure the upgrading from v3.1.1 succeed.
+func upgradeToVer46(s Session, ver int64) {
+	if ver >= version46 {
+		return
+	}
+	doReentrantDDL(s, "ALTER TABLE mysql.user ADD COLUMN `Reload_priv` ENUM('N','Y') DEFAULT 'N'", infoschema.ErrColumnExists)
+	doReentrantDDL(s, "ALTER TABLE mysql.user ADD COLUMN `File_priv` ENUM('N','Y') DEFAULT 'N'", infoschema.ErrColumnExists)
+	mustExecute(s, "UPDATE HIGH_PRIORITY mysql.user SET Reload_priv='Y' where Super_priv='Y'")
+	mustExecute(s, "UPDATE HIGH_PRIORITY mysql.user SET File_priv='Y' where Super_priv='Y'")
+}
+
 // updateBootstrapVer updates bootstrap version variable in mysql.TiDB table.
 func updateBootstrapVer(s Session) {
 	// Update bootstrap version.
diff --git a/session/session.go b/session/session.go
index 42ddb2729cd79..94b3c5fde5e9b 100644
--- a/session/session.go
+++ b/session/session.go
@@ -1829,7 +1829,7 @@ func CreateSessionWithDomain(store kv.Storage, dom *domain.Domain) (*session, er
 
 const (
 	notBootstrapped         = 0
-	currentBootstrapVersion = version45
+	currentBootstrapVersion = version46
 )
 
 func getStoreBootstrapVersion(store kv.Storage) int64 {