Molecular dynamics simulations were performed to analyze the water content dependence of the oxygen transport resistance through an ionomer thin film on a Pt surface, based on the phenomenological equations which make a correlation between the oxygen flux and the chemical potential. The oxygen transport resistance of the ionomer/Pt interface was found to be much larger than that of other regions, which indicated that the ionomer/Pt interface was dominant for oxygen transport through the ionomer thin film. Moreover, in the conventional method that assumes that the oxygen flux is driven by the concentration gradient, the oxygen transport resistance in the ionomer/Pt interface was found to be underestimated, whereas that in the ionomer/gas interface was found to be overestimated, which was caused by the exclusion of the contribution of the oxygen-film interaction on the oxygen flux. Furthermore, the oxygen transport resistance of the ionomer thin film increased with increasing water content. In particular, in the ionomer/Pt interface the transport resistance increased because the voids in the region were filled with water at a higher water content.