Polymer electrolyte fuel cell (PEFC) is focused worldwide as the energy conversion device for next generation. However, it has never been popular because of high price and low efficiency. In cathode catalyst layer of polymer electrolyte fuel cell, 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 ionomer interferes with oxygen permeation to the catalytic surface. The mechanism of oxygen permeation through the ionomer was not analyzed in detail because it is too small to research by experiment. In this research, we constructed the system including polymer electrolyte membrane, water molecule, oxonium ion and platinum surface by using molecular dynamics study, and researched about the effect of the water content of the ionomer on the structure of the ionomer and oxygen permeability.