In the operation of proton exchange membrane fuel cells, its ionomeric-polymer membrane is easily attacked by free radicals, resulting in the degradation of performance. In this work, the chemical degradation effect of hydrated Nafion membranes on gas adsorption, diffusion, and permeation behaviors is evaluated by molecular dynamics and Monte Carlo simulation. The correlation of pore ratio, free volume, hydrophilic/hydrophobic interface as well as the connectivity of the hydrophilic domain of Nafion membranes with gas transport characteristics are revealed. The results demonstrate that large free volume, high large pore ratio, smooth hydrophilic/hydrophobic interface, and good connectivity of the hydrophilic domain are favorable for adsorption, diffusion, and permeability processes. The C-S bond and C-O-C bond attack of membranes can increase the gas adsorption amount, which becomes weak after the tertiary carbon is attacked.