diff --git a/flow/connectors/bigquery/merge_stmt_generator.go b/flow/connectors/bigquery/merge_stmt_generator.go
index cca68cdda7..a6eb395026 100644
--- a/flow/connectors/bigquery/merge_stmt_generator.go
+++ b/flow/connectors/bigquery/merge_stmt_generator.go
@@ -101,16 +101,26 @@ func (m *mergeStmtGenerator) generateFlattenedCTE() string {
 		m.syncBatchID, m.dstTableName)
 }
 
-func (m *mergeStmtGenerator) transformedPkeyStrings() []string {
+// This function is to handle
+func (m *mergeStmtGenerator) transformedPkeyStrings(forPartition bool) []string {
 	pkeys := make([]string, 0, len(m.normalizedTableSchema.PrimaryKeyColumns))
 	for _, col := range m.normalizedTableSchema.Columns {
 		if slices.Contains(m.normalizedTableSchema.PrimaryKeyColumns, col.Name) {
 			pkeyCol := col.Name
 			switch qvalue.QValueKind(col.Type) {
 			case qvalue.QValueKindJSON:
-				pkeys = append(pkeys, fmt.Sprintf("TO_JSON_STRING(%s)", m.shortColumn[pkeyCol]))
+				if forPartition {
+					pkeys = append(pkeys, fmt.Sprintf("TO_JSON_STRING(%s)", m.shortColumn[pkeyCol]))
+				} else {
+					pkeys = append(pkeys, fmt.Sprintf("TO_JSON_STRING(_t.%s)=TO_JSON_STRING(_d.%s)",
+						pkeyCol, m.shortColumn[pkeyCol]))
+				}
 			default:
-				pkeys = append(pkeys, m.shortColumn[pkeyCol])
+				if forPartition {
+					pkeys = append(pkeys, m.shortColumn[pkeyCol])
+				} else {
+					pkeys = append(pkeys, fmt.Sprintf("_t.%s=_d.%s", pkeyCol, m.shortColumn[pkeyCol]))
+				}
 			}
 		}
 	}
@@ -128,9 +138,8 @@ func (m *mergeStmtGenerator) generateDeDupedCTE() string {
 			WHERE _peerdb_rank=1
 	) SELECT * FROM _dd`
 
-	shortPkeys := m.transformedPkeyStrings()
-	pkeyColsStr := fmt.Sprintf("(CONCAT(%s))", strings.Join(shortPkeys,
-		", '_peerdb_concat_', "))
+	shortPkeys := m.transformedPkeyStrings(true)
+	pkeyColsStr := strings.Join(shortPkeys, ", '_peerdb_concat_' ")
 	return fmt.Sprintf(cte, pkeyColsStr)
 }
 
@@ -164,11 +173,7 @@ func (m *mergeStmtGenerator) generateMergeStmt(unchangedToastColumns []string) s
 	}
 	updateStringToastCols := strings.Join(updateStatementsforToastCols, " ")
 
-	pkeySelectSQLArray := make([]string, 0, len(m.normalizedTableSchema.PrimaryKeyColumns))
-	for _, pkeyColName := range m.normalizedTableSchema.PrimaryKeyColumns {
-		pkeySelectSQLArray = append(pkeySelectSQLArray, fmt.Sprintf("_t.%s=_d.%s",
-			pkeyColName, m.shortColumn[pkeyColName]))
-	}
+	pkeySelectSQLArray := m.transformedPkeyStrings(false)
 	// t.<pkey1> = d.<pkey1> AND t.<pkey2> = d.<pkey2> ...
 	pkeySelectSQL := strings.Join(pkeySelectSQLArray, " AND ")