•Sulfonated poly (arylene ether sulfone)s containing 3,4-difluoro-phenyl moiety were successfully synthesized as PEM.•Comparing to SPAES-6FBPA-40, 2F-SPAES-40 membrane exhibited higher proton conductivity and greater microphase separation.•3,4-difluoro-phenyl side group is in favor for promoting phase separation to enhance proton conductivity and oxidative stability.Novel sulfonated poly(arylene ether sulfone) polymers with 3,4-difluoro-phenyl group (2F-SPAES-xx) were successfully synthesized via the direct copolymerization of 3,3′-disulfonate-4,4′-dichlorodiphenylsulfone, 4,4-dichlorodiphenylsulfone and 3,4-difluoro-phenyl hydroquinone. The polymers with different sulfonation degree were prepared by changing the mole ratio (20%–40%) of sulfonated monomer in the polymerization reaction. The proton conductivity, thermal and oxidative stability, mechanical properties, water uptake, swelling ratio, phase-separated morphology of the membranes were explored. The 2F-SPAES-40 membrane showed higher proton conductivity and better phase separation, oxidative stability than that of sulfonated poly(arylene ether sulfone) membrane (SPAES-6FPA-40). The proton conductivity of 2F-SPAES-40 membrane was up to 0.142 Scm− 1 at 80 °C in wet. These results indicated that incorporation of hydrophobic 3,4-difluoro-phenyl side group enhanced the oxidative stability and improved the proton conductivity by promoting the phase separation.