In order to study the microstructure of the prepared potential proton exchange membrane (PEM), molecular dynamics (MD) simulations were used to lucubrate the transport behavior of water molecules and hydronium ions inside the hydrated sulfonated styrene grafted fluorinated ethylene propylene (FEP) membrane, which possess different side chain lengths. By evaluating the radial distribution functions (RDFs), it was observed that with increasing side chain length, the average sulfur-hydronium ion separation slightly increased and the coordination number of H3O+ around sulfonic acid groups decreased whereas larger water clusters formed. The results of the mean square displacements (MSDs) show that the proton conductivities of the membranes with the proposed side chain lengths were about three fifths of the experimental data, of which the membrane with side chain length of 7 sulfonic styrene units was supposed to exhibit the highest proton conductivity, that is 115.69 mS cm(-1). All of the supposed membrane models presented good proton conductivity that could definitely meet the application requirements of the proton exchange membranes. The MD simulations can provide an insight to the chain structure of the radiation grafted membrane, and are of guidance significance to design other side-chain-structure polymers to be used as PEMs in proton exchange membrane fuel cells (PEMFCs). (C) 2017 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.