Graphene oxide (GO), owing to its atomic thickness and tunable physicochemical properties, exhibits fascinating properties in membrane separation fields, especially in water treatment applications (due to unimpeded permeation of water through graphene-based membranes). Particularly, GO-based membranes used for desalination via pervaporation or nanofiltration have been widely investigated with respect to membrane design and preparation. However, the precise construction of transport pathways, facile fabrication of large-area GO-based membranes (GOMs), and robust stability in desalination applications are the main challenges restricting the industrial application of GOMs. This review summarizes the challenges and recent research and development of GOMs with respect to preparation methods, the regulation of GOM mass transfer pathways, desalination performance, and mass transport mechanisms. The review aims to provide an overview of the precise regulation methods of the horizontal and longitudinal mass transfer channels of GOMs, including GO reduction, interlayer cross-linking, intercalation with cations, polymers, or inorganic particles, etc., to clarify the relationship between the microstructure and desalination performance, which may provide some new insight regarding the structural design of high-performance GOMs. Based on the above analysis, the future and development of GOMs are proposed.