The hydrogen (H2) crossover significantly impacts the performance and durability of proton exchange membrane fuel cells (PEMFCs). However, understanding the intricate dynamics of local H2 crossover in fuel cells is challenging due to complex transport and reactions. This study introduces advanced two-phase, three-dimensional PEMFCs transient models, incorporating H2 dissolution, diffusion/convection, and surface reactions, providing a comprehensive analysis of the interplay between H2 crossover and local charge, mass and heat. The study emphasizes the substantial influence of geometric and operational parameters on both H2 crossover flux and distribution uniformity by adjusting local membrane water and H2 concentrations. Elevated H2 crossover flux is often accompanied by non-uniform distribution, particularly noticeable under conditions of elevated temperature, backing pressure, and relative humidity (RH). Sensitivity analysis reveals load-dependent parameter effects, with RH exerting the most significant impact at lower loads compared to temperature and pressure, with its effect diminishing at higher loads. Additionally, H2 crossover results in 1–10 mV decrease in dynamic voltage loss but 20–57 mV increase in steady-state voltage loss. The steady voltage loss diminishes notably with increasing current load before slightly rising 1–3 mV, attributed to reduced activation overpotential for the oxygen reduction reaction utilizing excess electrons and protons from permeated H2. The subsequent increase is associated with heightened ohmic polarization losses due to membrane dehydration at elevated catalyst layer temperatures near the channel. This study contributes to advancing our understanding of H2 crossover, providing valuable insights for the development of mitigation strategies in fuel cell operation.