Is there any alternate way that direct bank entry can be reconcile ?

because in the both the statement there is an entry in one bank Debit and another bank Credit so if those entry can directly reconcile....

This is the way we recommend so you. An verify each transaction happened. Automatic reconciliation would prevent this from happening and most likely raise questions for an auditor. You need to verify the money came out (Bank A) and later went in (Bank B) as two separate reconcilations with two separate statements.

@Ray Carnes... Thanks for clarifications.