With the increasing need for high power density of proton exchange membrane fuel cells, new composite membranes have been explored for superior proton transport and gas impermeability. These membranes’ physicochemical properties usually deviate from existing empirical formulas, which are poorly understood, especially when mechanical deformation occurs. This poor understanding hinders development of novelty membranes and their fuel cell applications. Here, using polytetrafluoroethylene reinforced ionomer membrane as an example, we conducted extensive water absorption experiments to determine hydration levels at different water activities. Molecular dynamics simulations and electrochemical impedance spectroscopy were used to investigate the impacts of hydration level, external electric field strength, and tensile deformation on proton transport and electroosmotic drag coefficient, as well as the impact of hydration level and free volume ratio on oxygen permeability. We proposed mathematical correlations for these impacts and incorporated them into a single-cell voltage model to analyze their effects on fuel cell performance. Results show that an increase in the electric field strength alters the proton transport pattern, but has minimal impact on the electro-osmosis coefficient. The oxygen permeability coefficient of a deformed membrane with a free volume ratio of 28.57% is more than two orders of magnitude higher than that of a non-deformed membrane. The electro-osmatic drag coefficient imposes a larger influence on fuel cell performance than oxygen permeability