Polymer electrolyte membrane fuel cell (PEFC) is focused worldwide as the energy conversion device of next generation. In the PEFC cathode catalyst layer, an ionomer with which the catalyst is covered is very important on the point of transferring protons to the catalytic surface on the cathode side. On the other hand, it is said that an ionomer interferes with oxygen permeation to the catalytic surface. The mechanism of oxygen permeation through an ionomer was not analyzed in detail because it is too small to research by experiment. Moreover molecular dynamics simulation of the catalyst layer and oxygen permeability has not yet studied. In this research, we constructed the system including nafion, water, oxonium ion, platinum layers by using molecular dynamics study, and studied about the effect of the water content of the ionomer on the structure of the ionomer and permeability of the oxygen molecule. As the results, a lot of oxygen molecules permeated through a dried ionomer and reached to the catalytic surface but there were few oxygen molecules that permeated through a hydrated ionomer and reached there. In addition, it is found that the shape of the ionomer in the case of water content rate γ = 3, 7, 11 changed.