Transport-induced thermodynamic irreversibilities remain one of the primary factors limiting the efficiency and high-load performance of proton exchange membrane fuel cells (PEMFCs). However, the complex interactions among flow-field architecture, coupled transport phenomena, electrochemical reactions, and exergy destruction are not yet fully understood. This study presents an exergy-guided three-dimensional multiphysics framework that integrates electrochemical kinetics, multicomponent species transport, heat transfer, two-phase flow, membrane hydration, and entropy-generation analysis to investigate transport irreversibilities in hierarchical PEMFC flow-field architectures. The developed framework establishes direct quantitative relationships between flow-field geometry, local transport behavior, and exergy destruction mechanisms under realistic operating conditions. The results show that total exergy destruction increases from 0.14 to 1.10 W cm-2 as current density increases, while exergy efficiency decreases by approximately 40%–50% because of intensified mass-transport limitations. The optimized multiscale flow-field architecture improves net power density by up to 19% and exergy efficiency by 24%, while simultaneously reducing pressure losses by 20%–25% and increasing oxygen concentration by 6%–8% compared with the conventional design. Furthermore, transport-related irreversibilities become dominant above approximately 1.5 A cm-2, where mass-transfer resistance and viscous dissipation together account for more than 30%–35% of the total exergy destruction. These findings demonstrate that the proposed exergy-guided multiphysics framework provides a physically consistent strategy for identifying dominant transport-loss mechanisms and optimizing PEMFC flow-field architectures for enhanced electrochemical and thermodynamic performance.