The dynamic response of proton exchange membrane fuel cell (PEMFC) is an appropriate metric for evaluating the vehicle’s PEMFC system. In this study, we compare the experimental results of two stacks, each with an effective area of 102.66 cm2 (14.5cm×7.08cm), and bipolar plates featuring parallel two-dimensional straight channel (2D) and three-dimensional wave channel (3D). We specifically investigate the effects of load mode, load change, stoichiometric ratio, temperature, back pressure, and humidity on the output performance of both stacks, using polarization curve and electrochemical impedance spectroscopy (EIS). The 3D wave channel outperforms the 2D straight channel in terms of reaction gas dispersion, enhancement of diffusion and mass transfer to the diffusion layer, reduction of concentration polarization in the PEMFC, and improved self-humidification under low humidity conditions. More importantly, our results show that the implementation of a 3D wave channel results in both an enhanced steady-state performance and improved dynamic response for the PEMFC.