To know the movement of water in the Polymer Electrolyte Fuel Cell (PEFC) is important for deciding the optimum shape of the cell and the operating condition. It is well known that the PEFC shows the best performance under a moderate relative humidity condition. However, the experimental measurement is difficult because of the flow through the complex geometry of the diffusion layer. Therefore, in order to know the movement of water in the PEFC, a microscopic analysis was performed by a lattice gas automata (LGA) method. The influence of gas diffusion prevention by water was investigated. In addition, the relationship between the reaction time and the reaction quantity for a PEFC with a dry membrane was investigated. The reaction quantity, which had increased due to the membrane getting more wet by water generation, decreased due to the prevention of gas diffusion by water, and after a while, it settled into a steady state. According to the channel shape, distribution of water was observed in the diffusion layer and it affected the distribution of oxygen and hydrogen reaction quantity. Moreover, since the influence of the gas diffusion prevention by water on the cathode side was more dominant than that on the anode side, it was shown that the concentration overpotential of the cathode side strongly affects a cell performance.