Ordered structural modifications of the gas diffusion layer (GDL) are crucial for enhancing the performance of proton exchange membrane (PEM) fuel cells. In this work, a threedimensional, two-phase numerical model of PEM fuel cells with grooves added is constructed. The size, position, and direction of the grooves are examined. The essential relationship between grooves and the cell performance is revealed. The mechanisms of oxygen transport and water drainage are elucidated based on the Sherwood (Sh) number and capillary pressure gradient (∇P C ), respectively. The findings suggest that under-rib longitudinal grooves offer lower cell performance than under-channel longitudinal grooves due to on-way resistance. Furthermore, the smaller the size of grooves, the higher the cell performance. The underlying reason is that the longitudinal groove demonstrates an increased Sh average and an enhanced ∇P C,average , while the transverse groove exhibits a reduced Sh average and a progressively smooth ∇P C,local , respectively. On this basis, a comparison between longitudinal and transverse grooves is performed. The current density is enhanced by 0.89% and 1.10%, respectively. Longitudinal grooves are recommended in industrial practice owing to the more favorable ∇P C,average and relative ease of fabrication. Finally, the superior effects of the longitudinal groove on the cell performance are explored via applications in GDLs with various properties. Taking the drainage capability into account, the longitudinal groove is more suitable for addition in GDLs with a lower porosity.