Graphene oxide (GO) membrane, bearing well-aligned interlayer nanochannels and well-defined physicochemical properties, promises fast proton transport. However, the deficiency of proton donor groups on the basal plane of GO and weak interlamellar interactions between the adjacent nanosheets often cause low proton conduction capability and poor water stability. Herein, we incorporate sulfonated graphene quantum dots (SGQD) into  GO membrane to solve the above dilemma via synergistically controlling the edge electrostatic interaction and in-plane π–π interaction of SGQD with GO nanosheets. SGQD with three different kinds of electron-withdrawing groups are employed to modulate the edge electrostatic interactions and improve the water swelling resistant property of GO membranes. Meanwhile, SGQD with abundant proton donor groups assemble on the sp2 domain of GO via in-plane π–π interaction and confer the GO membranes with low-energy-barrier proton transport channels. As a result, the GO membrane achieves an enhanced proton conductivity of 324 mS cm–1, maximum power density of 161.6 mW cm–2, and superior water stability when immersed into water for one month. This study demonstrates a strategy for independent manipulation of conductive function and nonconductive function to fabricate high-performance proton exchange membranes.