Flow field structure can largely determine the output performance of Polymer electrolyte membrane fuel cell. Excellent channel configuration accelerates electrochemical reactions in the catalytic layer, effectively avoiding flooding on the cathode side. In present study, a three-dimensional, multi-phase model of PEMFC with a 3D wave flow channel is established. CFD method is applied to optimize the geometry constructions of three-dimensional wave flow channels. The results reveal that 3D wave flow channel is overall better than straight channel in promoting reactant gases transport, removing liquid water accumulated in microporous layer and avoiding thermal stress concentration in the membrane. Moreover, results show the optimal flow channel minimum depth and wave length of the 3D wave flow channel are 0.45 mm and 2 mm, respectively. Due to the periodic geometric characteristics of the wave channel, the convective mass transfer is introduced, improving gas flow rate in through-plane direction. Furthermore, when the cell output voltage is 0.4 V, the current density in the novel channel is 23.8% higher than that of conventional channel. •A novel 3D wave flow channel is introduced to enhance the PEMFC performance.•The geometrical structure of 3D wave channel is optimized.•Current density in novel channel is 23.8% higher than conventional channel at 0.4 V.