The chemical and morphological structure of polymer electrolyte directly determines their properties applied as proton exchange membrane. Different chemical structure design of sulfonated poly (arylene ether sulfone) may result in different morphological structure and properties. In this article, three sulfonated poly (arylene ether sulfone)s with similar backbone but varied side groups, that is, with fluoropheny side group (SEF), cyanogroupson side group (SEB) and without any side group introduction (SES), were cast into membranes. The properties such as the proton conductivity, water uptake, dimensional stability, microstructure and H-2/O-2 single cell performance of the membranes were characterized and compared with each other. The proton conductivities of them did not show much diversity, ranging from 0.158 to 0.197 S/cm, while the performance of a single proton exchange membrane fuel cell exhibited great difference, the maximum power density of the SEF and SEB reached 115.5mw/cm(2) and 94.7 mw/cm(2) compared to 72.5 mw/cm(2) for SES. From the microstructure images, the smaller size of separated hydrophobic domains, cross-linked and more uniform distribution of hydrophilic domains was observed in SEF and SEB than in SES. The results indicated that the introduction of suitable side group, such as fluorophenyl, to sulfonated poly (arylene ether sulfone) might contribute to its overall performance as one of candidate materials for proton exchange membrane. Copyright (C) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.