Electrode structure plays an important role on performance of the proton exchange membrane (PEM) fuel cell. A two-dimensional, two-phase flow model is presented to simulate the performance of PEM fuel cell with direct flow fields and its mass transfer in cathode in this paper. Effects of depth and width of channel and depth of gas diffusion layer on the performance of PEM fuel cell and mass transfer in its cathode are analyzed. The results show that electrode structure affects strongly the performance of fuel cell and mass transfer in its electrode; when depth of channel is 0.75mm, there are the worst performance and mass transfer; decreases of the width of the channel and depth of the gas diffusion layer are beneficial to improving mass transfer and increase performance of PEM fuel cell. These results are very helpful for optimization of PEM fuel cells.