The heat generation in PEMFC is proportional to the electrical power output. Therefore, when the fuel cell produced the maximum output, the maximum heat was generated. In order to maintain the performance of the fuel cell, thermal management is as important as pressure and humidity conditions of the reactive gas. In this study, considering the thermal management for the maximum output operation, the optimal cooling channel design specifications of bipolar plate are found for the highest cooling performance. In the current bipolar plate research, many studies focused on analyzing various factors individually but there is no more study on the interaction between design factors. In this study, the heat transfer was simulated by COMSOL Multiphysics with the main design factors which are designated shape, width and rib length. One of the experimental design methods, general full factorial design method, was used to analyze the main factor and interaction on average temperature and maximum temperature for the design specification of fuel cell bipolar plate. When analysis result shows that all of these three factors are highly important, it can confirm that the interaction occurs between the factors.