Dear Pradeepkumar,
You can change the name of your son.
Birth Certificate issued by the competent authorities with name of baby of your choice,father and mother name is important for education etc. which will solve the problem throughout your/his life.
So, I suggest you to obtain a fresh birth certificate from appropriate authorities from your area. If they have issued birth certificate mentioning the name of baby of your choice which you require in future. It will solve the problem for you and your baby.
If birth certificate already issued by the competent authority of your baby which does not contain the name of your choice( which you required). Visit to birth certificate issuing authority,obtain application and fill up all the col.+ affidivit duly notarised regarding change of your son and submit for issue of revised.birth certificate of your baby.
I hope the matter is clear to you.
Nagaraj N Nyamati