Performance heterogeneity in proton exchange membrane fuel cells (PEMFCs), which includes both inconsistency and inplane non-isopotential behavior, is a critical issue influenced by operating parameters. However, few studies have systematically explored the potential coupling between the non-isopotential behavior within a single cell and the performance inconsistency across a full stack. This study utilizes a commercial U-shaped PEMFC stack to experimentally assess how loading rate, cathode stoichiometric ratio, and cathode back pressure affect performance heterogeneity. The results reveal that cells located at the stack’s edges are more susceptible to non-isopotential behavior due to uneven distributions of saturated water and oxygen. A strong coupling effect between intra-cell non-isopotentiality and inter-cell performance variation was also identified. While increasing back pressure and oxygen availability improves overall stack performance and uniformity, the optimal conditions for maximizing performance do not perfectly align with those for minimizing heterogeneity. These findings provide valuable insights into the internal heterogeneity of PEMFCs and establish a solid foundation for performance optimization in future applications.