The design of the flow field plate plays a crucial role in the performance of proton exchange membrane fuel cell (PEMFC). In this study, a novel three-dimensional stepped wavy flow field (SWFF) is developed to enhance the output performance of PEMFC. The effects of geometric parameters of this novel flow field, included the total stepped length (S) and depth (H), the ratio of the sub-stepped length (s1:s2 and s1:s3), and the ratio of the sub -stepped depth (h1:h2), on the transport and distribution characteristics of oxygen and water in PEMFC are numerically investigated. The results demonstrated that the smaller stepped total length and larger stepped total depth result in better cell performance. In addition, the output performance of PEMFC increases with the rise of the ratio of s1:s2, and the decrease of the ratio of s1:s3 under the optimal total stepped length and depth. It is also worth noting that the output performance of PEMFC first increases and then decreases with the rise of the ratio of h1:h2. The optimal values for S, H, s1, s2, s3, h1 and h2 are 8 mm, 0.8 mm, 1.6 mm, 1.6 mm, 1.6 mm, 0.4 mm and 0.4 mm, respectively. Furthermore, when compared to the rectangular baffle flow field, wavy flow field, and parallel flow field, the 3D stepped wavy flow field demonstrated a significant increase in the maximum net output power with improvements of 4.8 %, 11.3 %, and 27.9 %, respectively.