Shakhbut married twice. His first wife was his first cousin, Sheikha Fakhera bint Hazza Al Nahyan, and she was the mother of all his children. They had two sons, Saeed and Sultan. Both of his sons predeceased Shakhbut; they died in their youth while living in exile with their father. The elder son, Saeed, was married to his cousin, the daughter of his uncle
Sheikh Zayed in
Buraimi in 1963. He has a son named Tahnoun. Saeed's daughter, Fakhra is married to
Nahyan bin Mubarak Al Nahyan. Sultan also had a son, Khalifa.{{cite journal|author=Miriam Joyce|title=On the road towards unity: the Trucial states from a British perspective, 1960–66|journal=
Middle Eastern Studies|year=1999 After being deposed, Shakhbut and his family went into exile to Iran under his brother Zayed's orders. They resided in the
Khuzestan province of Iran. They were hosted by Sheikh Abdulkarim Al-Faisali of the
Banu Tamim tribe. ==Honours==