Dear Amit,
To make change history and tracking through standard SAP, you may consider to implement Engineering Change Management or ECM for the BOMs.
You will have to check OS27 and OS25 configuration settings. ECM will allow you to change or create any BOM depending upon the BOM usage and BOM status with reference to a change master.
Otherwise, if you have to implement total custom logic, you will have to use customer exits/user exits or BAdI's.
Please check:
https://scn.sap.com/thread/997101
Best Regards,
Rajen