Proton exchange membranes with high ionic conductivity and good chemical stability are critical for achieving high power density and long lifespan of direct methanol cells (DMFCs). Herein, a zwitterionic molecule was grafted onto the surface of polyvinylidene fluoride (PVDF) nanofibers to obtain functionalized PVDF porous substrate (SBMA-PDA@PVDF). Then, sulfonated poly(ether ether ketone) (SPEEK) was filled into the pores of SBMA-PDA@PVDF, and further ionic cross-linked via H2SO4 to prepare the composite membrane (SBMA-PDA@PVDF/SPEEK). The basic groups on the zwitterionic interface could not only establish ionic cross-linking with SPEEK to increase chemical stability and reduce swelling, but also serve as the adsorption sites for subsequent H2SO4 cross-linking to significantly enhance proton conductivity. Super-high proton conductivity (165.34 mS cm−1, 80 °C) was achieved for the membrane, which was 2.12 times higher than that of the pure SPEEK. Moreover, the SBMA-PDA@PVDF/SPEEK membrane exhibited remarkably improved oxidative stability of 91.6 % mass retention after soaking in Fenton’s agent for 12 h, while pure SPEEK completely decomposed. Satisfactorily, the DMFC assembled with SBMA-PDA@PVDF/SPEEK exhibited a peak power density of 99.01 mW cm−2, which was twice as much as that of commercial Nafion 212 (48.88 mW cm−2). After 235 h durability test, only 11 % voltage loss was observed.