This study aims to optimize the flow channel design for a proton exchange membrane electrolyzer cell (PEMEC) to minimize the pressure drop across the cell. The pattern of parallel flow channels is considered with a dual-porous layer structure sandwiched between the flow channel plate and the catalyst layer. Four geometric factors are considered in the optimization analysis, including the width of the flow channel, the depth of the flow channel, the particle diameter of the large-pore porous layer, and the particle diameter of the small-pore porous layer. Computational fluid dynamics (CFD) is used to simulate the flow field, and based on the results of the CFD simulation, the Taguchi method is employed to analyze the optimal flow channel design. The importance of the factors is further analyzed by the analysis of variance (ANOVA) method. Three inlet velocities are assigned in the Taguchi analysis, which are 0.01, 0.1332, and 0.532 m/s, and then an orthogonal array is constructed and analyzed for each inlet flow condition. It is found that the optimal combination of the factors is the depth of the flow channel 1 mm, the width of the flow channel 3 mm, the particle diameter of the large-pore porous layer 0.212 mm, and the particle diameter of the small-pore porous layer 0.002 mm. The pressure drop across the PEMEC is minimized at the condition with the optimal combination of the factors. The ANOVA analysis shows that the depth of the flow channel exhibits the most significant impact on the pressure drop, while the other factors play minor roles only.