Bipolar plate is the key component of proton exchange membrane (PEM) fuel cell and represents a significant part of the overall cost and the total weight in a fuel cell stack. The thin sheet metal, with usually 0.1~0.3mm thickness, deformed to bipolar plate with flow channel 0.5~2mm width and depth, by rubber pad stamping can reduce the cost greatly. The rubber pad is simulated by solid element and hydraulic pressure respectively. Experiment shows that the hydraulic pressure can simulate the rubber pad. The thin sheet metal is modeled by solid element and shell element respectively. Considering thin sheet metal material size effect, the shell element cannot simulate the thin sheet metal stamping process because of small corner radius. Modeling rubber pad by hydraulic pressure and thin sheet metal by solid element, the simulation of the rubber pad stamping process shows that 1) the sheet metal in channel appears large uneven strain with high stress; 2) convex fillet make the sheet metal two direction tensions and should keep large fillet corner. Those simulations are validated by experiments. The research on rubber pad stamping will improve the understanding of this micro forming process and provide design guide of flow channel.