The shortage of freshwater and energy has proposed more stringent requirements for ion separation technology. Fortunately, membrane separation technology, based on graphene and its derivatives, has been widely applied in the research of biomedical, water treatment, and energy process. However, the trade-off between selectivity and permeability is considerably difficult for ion separation, which may limit the selectivity and permeability of ions. Herein, graphene-based separation membranes for ion separation are first introduced, including single-layer porous graphene membrane, multilayer stacked graphene-based membrane, and graphene oxide-based composite membrane. And the mechanisms of ion transport and separation in graphene-based membrane are also emphasized, such as solution diffusion, size sieving, electrostatic interaction, surface effect, etc. Moreover, the advances of graphene-based membranes for desalination, heavy metal separation, and lithium ions extraction are also highlighted. Finally, we propose some perspectives for the future development of graphene-based membranes in the field of ion separation for practical application. This review can provide a comprehensive perspective to understand and design graphene-based membranes for ion separation.