His first marriage was to the granddaughter of Raja Ali Khan Faruqi, King of Khandesh.[7] He next married at Lahore on 15 May 1587, Habiba Banu Begum Sahiba, daughter of Khan-i-Azam Mirza Aziz Koka, sometime Subahdar of Gujarat, Bengal and Malwa, and granddaughter of Akbar's foster father Shams ud-Din Ataga Khan.
From Habiba Begum he had three sons, Prince Rustam Mirza who was born at Lahore on 27 August 1588, Prince Alam Mirza who was also born at Lahore around 4 November 1590, and Prince Arbaham Alif Aziz Mirza who was born at Multan three years later on 7 October 1593. Prince Rustam, however, died in Lahore on 9 December 1597, at the age of 9. Prince Murad's daughter Iffat Jahan Banu Begum married Shahzada Parviz (son of his elder brother Jahangir). Besides the above, he had also married two Rajput princesses.