Employee Not Collecting His Gratuity Cheque - How To Proceed?

Since you have dismissed him even though after domestic enquiry, I guess he is plannng to challenge the dismissal before court, hence he is not showing any interest for receiving gratuity.
In this case follow the above mentioned steps as advised for payment of gratuity.

Dear Madhan,
You have strong case, so No Worry. Now you can send the Gratuity amount cheque to his residential address with Registered A.D. In case he returns the envelope without acceptance, keep the returned envelope as it is in his personal file without opening.
Same can be produced as an evidence in future, if required.
Regards,
Suresh