In order to understand the pressure effect on water mass fraction in the cathode for the PEM(Proton Exchange Membrane) fuel cell, a model was set up by three conservation equations, and it was considered the Gravity in source item. The modeling domain consists of the membrane, two catalyst layers, two diffusion layers, and two channels. It is simulation of species mass fraction in this paper. The results of simulation were drawn six pictures. On analyzing of pictures, it got conclusion as follow: Water mass fraction decreases along with pressure increasing in channel. Water mass fraction increases along with pressure increasing close to catalyst. Water mass fraction in cathode of fuel cell with anode-upward is higher than that with cathode-upward because of the effect of gravity.