KH. Husein Muhammad married with Nyai. Hj. Lilik Nihayah Fuadi. From this marriage, he was blessed with 5 sons and daughters. His children include Hilya Auliya born 1991, Layali Hilwa born 1992, Muhammad Fayyaz Mumtaz born 1994, Najla Hammaddah born 2002 and Fazla Muhammad born 2003.