In the development of more efficient and stable Polymer Electrolyte Fuel Cell (PEFC), it is important to propose the optimal component shape. In this study, our past model was improved, and simplified two-dimensional PEFC analysis model including flow and heat transfer of cooling water was made. And the influence by changing the thickness of membrane and gas diffusion layer (GDL) on the cell performance was calculated. As a result, we found that it is possible to improve the cell output by thinning the GDL more than the membrane in case of low voltage and by thinning the membrane more than the GDL in case of high voltage, but thinning the membrane and the GDL increased the current density distribution. In addition, by arranging the values of average current density and the current density distribution, the evaluation graphs were made, which became a help of the shape design in the membrane and the GDL.