With the escalating demand for electrochemical energy storage, commercial lithium-ion and metal battery systems have been increasingly developed. As an indispensable component of batteries, the separator plays a crucial role in determining their electrochemical performance. Conventional polymer separators have been extensively investigated over the past few decades. Nevertheless, their inadequate mechanical strength, deficient thermal stability, and constrained porosity constitute serious impediments to the development of electric vehicle power batteries and the progress of energy storage devices. Advanced graphene-based materials have emerged as an adaptable solution to these challenges, owing to their exceptional electrical conductivity, large specific surface area, and outstanding mechanical properties. Incorporating advanced graphene-based materials into the separator of lithium-ion and metal batteries has been identified as an effective strategy to overcome the aforementioned issues and enhance the specific capacity, cycle stability, and safety of batteries. This review paper provides an overview of the preparation of advanced graphene-based materials and their applications in lithium-ion, lithium-metal, and lithium-sulfur batteries. It systematically elaborates on the advantages of advanced graphene-based materials as novel separator materials and outlines future research directions in this field.