Conventional physics‐based fuel cell models have faced limitation in explaining the through‐plane liquid water distributions observed by state‐of‐the‐art imaging techniques. To elucidate these experimental findings, we advance a temperature‐dependent phase separation model (TDPSM) framework by introducing separate liquid transport equations for each porous constituent. The proposed theoretical framework incorporates relative hydrophobicity at overlapping interfaces and employs a volume‐averaging scheme to reveal the physics underlying optical liquid visualization. A novel validation approach is proposed, enabling simultaneous prediction of through‐plane liquid profiles and conventional polarization curves with strong agreement to experimental data. Extensive numerical simulations comparing water transport scenarios with and without a microporous layer (MPL) integrate previously fragmented experimental findings on the MPL’s dual role. The study also presents water management strategies for two operating regimes: (i) low‐temperature high‐humidity (LTHH), where liquid flooding dominates, and (ii) high‐temperature low‐humidity (HTLH), where membrane dehydration presents an emerging industrial challenge. Under LTHH conditions, a hydrophobicity order of catalyst layer (CL) > MPL > gas diffusion layer (GDL) establishes an interfacial liquid pump that enables effective liquid removal. In contrast, under HTLH operation, a more hydrophobic MPL relative to the CL (MPL > CL) forms an interfacial barrier that sustains reliable membrane water retention. Overall, this theoretical framework redefines water management as a synergistic outcome of relative hydrophobic characteristics between adjacent porous layers, rather than as properties of isolated components.