The side chain (SC) length of perfluorosulfonic acid (PFSA) reportedly influences the proton conductivity and mechanical strength of the membranes in the application of proton exchange membrane. Here, we conducted a series of molecular dynamics simulations to explore the effect of SC length on the morphology and mechanical properties of the PFSA membrane. The results of these simulations pointed to the stronger aggregation of the aqueous domain in the longer SC membranes. This leads to the swollen network structure of the aqueous domains at high water contents, rather than the tortuous layer structure observed in the shorter SC membrane. Furthermore, the mechanical simulation found that the longer SC membranes possessed lower and higher mechanical strengths than the shorter SC membranes at lower and higher water contents, respectively, resulting from the lower ionic strength and larger polymer domains. These findings will be useful for designing new materials for fuel cell applications. (C) 2018 Elsevier Ltd. All rights reserved.