Bhatt is the son of Nanabhai Bhatt (1915–1999), a Hindi film director and producer. His father was a Gujarati Brahmin and mother a Gujarati Muslim.[2] Nanabhai's brother, Balwant Bhatt (1909–1965) was also a Hindi film director. He is married to Nilima Bhatt. Bhatt has one daughter named Sakshi and a son Vishesh;[3]Vishesh Films was named after him. For 30 years Mukesh along with his brother Mahesh produced movies under the banner of Vishesh Films. However owing to differences between the brothers, Mukesh Bhatt took over Vishesh Films and in May 2021, it was publicly announced that Mahesh Bhatt was no more associated with the firm.[4][5]
He, along with his brother Mahesh, produced Mr. X (2015) and Hamari Adhuri Kahani (2015) with Emraan Hashmi and Vidya Balan in leading roles. It is based on the love story of Bhatt's parents Nanabhai Bhatt and Shirin Mohammad Ali, along with his stepmother.