The two-dimensional graphene has an ultra-thin lamellar structure, and the gap size of lamellar can intercept specific substances. Meanwhile, graphene can also be used as a protective layer on the surface for anti-oxidation due to excellent chemical stability. In recent years, modification of separation membrane properties by graphene-based materials has become a research hotspot in this field. The work aims to explore the application of graphene-based materials in membrane separation. The classification and preparation methods of graphene were briefly introduced. The mechanisms of graphene modification in the improvement of flux, selectivity, mechanical properties, thermal stability, anti-chlorine property and anti-fouling property for the membranes were discussed. The membrane modification was mainly conducted with graphene-based materials through doping or surface depositing. The modified membranes of graphene-based materials showed excellent separation performance in desalination, oil-water separation, dye decolorization, organic dehydration, trace volatile organic compounds removal from aqueous solutions, organic-organic separation and gas separation. The inner-layer and inter-layer space of the graphene-based materials can build the transport channels for the permeate. The functional groups and charges on the surface of graphene-based materials can enhance the affinity between the permeate and the modified membrane. Thus, the flux and selectivity can be improved simultaneously. It is proposed that the future research can focus on tailoring the structure of graphene-based materials, improving the compatibility of graphene-based materials in the polymer matrix and enhancing the stability of graphene-based materials modified membranes.