Effective reactant utilization, transport, and optimal water and thermal management are crucial for enhancing the performance of proton exchange membrane fuel cells. This study introduces a three-dimensional multiphase computational fluid dynamics (CFD) model to explore the combined effects of flow channel geometry and baffle configurations on PEMFC performance. First, the influence of various single-serpentine channel cross-sectional shapes, square, trapezoidal, dovetail, and triangular, was assessed. Second, different baffle designs, including typical baffles, baffles with a central hole, and perforated baffles, were incorporated into a square flow field to evaluate their impact. Finally, the performance implications of various flow field-baffle combinations were systematically analysed. The results indicate that the dovetail flow field yielded the highest performance, with a 10.47% increase in current density compared to the conventional square channel. Moreover, introducing typical baffles, baffles with central holes, and perforated baffles led to current density improvements of 5.86%, 6.21%, and 7.61%, respectively, relative to the standard flow channel without baffles. Notably, the optimal combination of channel geometry and baffle configuration enhanced fuel cell performance by up to 14.95%, minimizing pressure drop. These findings provide significant insights into the design of PEMFCs, highlighting the potential of integrated flow channel and baffle design to achieve superior performance.