Many researches have indicated that the side chain length of perfluorosulfonic acid (PFSA) polymers had nonnegligible effects on PFSA membrane properties. However, the effects have not been completely revealed yet. This paper uses molecular dynamics simulation to explore the effects of side chain length on the structure, oxygen transport and thermal conductivity of PFSA membrane. In PFSA membrane with longer side chains, the maximum size of water clusters is larger, while the connectivity of water clusters is poorer and size distribution of water clusters is more heterogenous. And the structural characteristics have a strong effect on the diffusion and solubility coefficient of oxygen molecules. The diffusion of oxygen molecules may be hindered due to the existence of small pores in PFSA membrane with longer side chains even at high water content, leading to a lower diffusion coefficient. In addition, with the increment of water content lambda, the solubility coefficient of oxygen molecules in PFSA membrane with shorter side chains decreases more quickly at lambda < 12, resulting in a most obvious difference of solubility coefficients for different side chain lengths when. is about 12. Moreover, the thermal conductivity of PFSA membrane with shorter side chains is higher. (C) 2019 The Electrochemical Society.