Amidinothiourea crosslinked graphene oxide membrane was prepared by a multilayer self-assembly method along with (3-aminopropyl) triethoxysilane modification, while different thicknesses of the membrane layer were obtained by regulating the volume of graphene oxide dispersion. The removal rate of the membrane layer with different thicknesses of heavy metal ions was explored and its removal mechanism was explained. The results show that the membrane can maintain high stability after 90 days of immersion in water. When the volume of graphene oxide dispersant increases from 9 ml to 15 ml, the thickness of the membrane layer enhances from about 120 nm to about 200 nm. After filtration of 140 ml of different nitrate solutions, the water fluxes of different membranes are about 22.6 l m−2 h−1·bar−1, 6.1 l m−2 h−1·bar−1, and 1.4 l m−2 h−1·bar−1, respectively. The removal rates of the preferred membrane for Pb2+, Cd2+, and Cu2+ are 43.3 %, 41.2 %, and 39.7 %, respectively. The ion removal mechanism is mainly due to the Dornan effect.