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Layer-by-layer (LbL) assembly of oppositely charged materials has been widely used as an approach to make two-dimensional (2D) nanosheet-based membranes, which often involves 2D nanosheets being alternately deposited with polymer-based polyelectrolytes to obtain an electrostabilized nanosheet-polymer structure. In this study, we hypothesized that using 2D nanosheets with matching physical properties as both polyanions and polycations may result in a more ordered nanostructure with better stability than a nanosheet-polymer structure. To compare the differences between nanosheet-nanosheet vs nanosheet-polymer structures, we assembled negatively charged molybdenum disulfide nanosheets (MoS2) with either positively charged graphene oxide (PrGO) nanosheets or positively charged polymer (PDDA). Using combined measurements by ellipsometer and quartz crystal microbalance with dissipation, we discovered that the swelling of MoS2-PrGO in ionic solutions was 60% lower than that of MoS2-PDDA membranes. Meanwhile, the MoS2-PrGO membrane retained its permeability upon drying, whereas the permeability of MoS2-PDDA decreased by 40% due to the restacking of MoS2. Overall, the MoS2-PrGO membrane demonstrated a better filtration performance. Additionally, our X-ray photoelectron spectroscopy results and analysis on layer density revealed a clearer transition in material composition during the LbL synthesis of MoS2-PrGO membranes, and the X-ray diffraction pattern suggested its resemblance to an ordered, layer-stacked structure. In conclusion, the MoS2-PrGO membrane made with nanosheets with matching size, shape, and charge density exhibited a much more aligned stacking structure, resulting in reduced membrane swelling under high salinity solutions, controlled restacking, and improved separation performance.