Understanding the nanostructure of ionomer membranes is important for elucidating the mechanism oftheir molecular transport properties and for improving the performance of proton exchange membranefuel cells. In this study, we incorporated a ring structure into the main chain of perfluorinated sulfonicacids ionomers including short side chain (SSC) as a highly oxygen-permeable ionomer and used moleculardynamics simulations to investigate the interrelation between the structural properties of the ionomerand its transport properties. The incorporated ring structure influences the stiffness of the ionomerchain and the nanostructure of the ionomer membrane. To demonstrate the influence of the ionomerstructure on the transport properties and the nanostructural features such as water channels, the structureand water volume were analyzed and the water-cluster connectivity was calculated for modified SSCionomers and long side chain (LSC) ionomer, and the results were compared. Compared with the LSCionomer, the modified SSC ionomer exhibits better oxygen transport properties but worse water transportproperties because of its stiff chain derived from the ring structure.