The working temperature affects the performance of PEMFC, so a reasonable and efficient cooling channel is necessary to control the working temperature in an efficient area. In this study, the channel structure of the bipolar plate for PEMFC is analyzed using the FLUENT simulation calculation method. The influence of cell size and cooling water flow direction on cell temperature distribution is analyzed, including an examination of the channel ridge width, depth, and aspect ratio of the bipolar plate. After comparing and analyzing three ridge width sizes (0.5 mm, 1.5 mm and 2 mm) in the paper, it was found that a ridge width of 2 mm had the best heat transfer performance. And it was found that a groove depth of 0.5 mm had the best heat transfer performance when comparing three groove depth dimensions (0.5 mm, 1 mm and 1.5 mm). The aspect ratio size parameters had almost no effect on the maximum and average temperatures of the electric stacks, while the relative flow direction of cooling water had a great influence on the temperature distribution of the bipolar plate.