diff --git a/pkg/proxy/client_conn.go b/pkg/proxy/client_conn.go
index da134e30d92b9..974be97e46411 100644
--- a/pkg/proxy/client_conn.go
+++ b/pkg/proxy/client_conn.go
@@ -107,7 +107,8 @@ type ClientConn interface {
 }
 
 type migration struct {
-	setVarStmts []string
+	setVarStmtMap map[string]struct{}
+	setVarStmts   []string
 }
 
 // clientConn is the connection between proxy and client.
@@ -231,6 +232,7 @@ func newClientConn(
 		}
 		c.tlsConfig = tlsConfig
 	}
+	c.migration.setVarStmtMap = make(map[string]struct{})
 	return c, nil
 }
 
@@ -408,6 +410,17 @@ func (c *clientConn) handleKill(e *killEvent, resp chan<- []byte) error {
 // handleSetVar handles the set variable event.
 func (c *clientConn) handleSetVar(e *setVarEvent) error {
 	defer e.notify()
+	_, ok := c.migration.setVarStmtMap[e.stmt]
+	if ok {
+		for i := 0; i < len(c.migration.setVarStmts); i++ {
+			if c.migration.setVarStmts[i] == e.stmt {
+				c.migration.setVarStmts = append(c.migration.setVarStmts[:i], c.migration.setVarStmts[i+1:]...)
+				i--
+			}
+		}
+	} else {
+		c.migration.setVarStmtMap[e.stmt] = struct{}{}
+	}
 	c.migration.setVarStmts = append(c.migration.setVarStmts, e.stmt)
 	return nil
 }
diff --git a/pkg/proxy/client_conn_test.go b/pkg/proxy/client_conn_test.go
index 556d38f160fa2..1948d6a605728 100644
--- a/pkg/proxy/client_conn_test.go
+++ b/pkg/proxy/client_conn_test.go
@@ -568,3 +568,41 @@ func TestClientConn_SendErrToClient(t *testing.T) {
 	cc.SendErrToClient(moerr.NewInternalErrorNoCtx("msg1"))
 	wg.Wait()
 }
+
+func TestHandleSetVar(t *testing.T) {
+	defer leaktest.AfterTest(t)()
+	var cc clientConn
+	cc.migration.setVarStmtMap = make(map[string]struct{})
+	e0 := &setVarEvent{
+		baseEvent: baseEvent{waitC: make(chan struct{}, 5)},
+		stmt:      "set autocommit=0",
+	}
+	require.NoError(t, cc.handleSetVar(e0))
+	require.Equal(t, 1, len(cc.migration.setVarStmtMap))
+	require.Equal(t, 1, len(cc.migration.setVarStmts))
+	require.Equal(t, e0.stmt, cc.migration.setVarStmts[len(cc.migration.setVarStmts)-1])
+
+	require.NoError(t, cc.handleSetVar(e0))
+	require.Equal(t, 1, len(cc.migration.setVarStmtMap))
+	require.Equal(t, 1, len(cc.migration.setVarStmts))
+	require.Equal(t, e0.stmt, cc.migration.setVarStmts[len(cc.migration.setVarStmts)-1])
+
+	e1 := &setVarEvent{
+		baseEvent: baseEvent{waitC: make(chan struct{}, 5)},
+		stmt:      "set autocommit=1",
+	}
+	require.NoError(t, cc.handleSetVar(e1))
+	require.Equal(t, 2, len(cc.migration.setVarStmtMap))
+	require.Equal(t, 2, len(cc.migration.setVarStmts))
+	require.Equal(t, e1.stmt, cc.migration.setVarStmts[len(cc.migration.setVarStmts)-1])
+
+	require.NoError(t, cc.handleSetVar(e0))
+	require.Equal(t, 2, len(cc.migration.setVarStmtMap))
+	require.Equal(t, 2, len(cc.migration.setVarStmts))
+	require.Equal(t, e0.stmt, cc.migration.setVarStmts[len(cc.migration.setVarStmts)-1])
+
+	require.NoError(t, cc.handleSetVar(e1))
+	require.Equal(t, 2, len(cc.migration.setVarStmtMap))
+	require.Equal(t, 2, len(cc.migration.setVarStmts))
+	require.Equal(t, e1.stmt, cc.migration.setVarStmts[len(cc.migration.setVarStmts)-1])
+}