Mass transport polarization induced by water blockage within the gas diffusion layer (GDL) of proton exchange membrane fuel cells (PEMFCs) constitutes a critical bottleneck limiting high-current-density performance. This study establishes a model of water invasion under compression and thickness changes, facilitated by in-situ X-ray computed tomography (X-CT) imaging and finite element modeling based on realistic geometric structures. Subsequently, it investigates the gas transport under liquid saturation. Extraction of the pore network model (PNM) reveals that both compression and water flooding significantly reduce the mean pore diameter, while exerting minimal impact on the coordination number. The results indicate that liquid water transport pathways exhibit scale-dependent characteristics. Furthermore, the effective diffusion coefficient (EDC) and permeability (K) vary linearly with thickness. Notably, 40 % compression causes an 80 % reduction in permeability, while significantly mitigating the pressure drop phenomenon. This work provides multiscale insights into mass transport limitations across various porous media.