Proton exchange membrane fuel cells (PEMFCs) are highly susceptible to performance limitations at high current densities due to competing gas and liquid transport mechanisms. While microporous layers (MPLs) reduce contact resistance, they often exacerbate the risk of flooding. This study leverages the topological advantages of highly interconnected cage-like MPLs. By integrating X-ray computed tomography (X-CT) with digital techniques (reconstructed geometry and numerical simulation), it reveals the mass transfer mechanisms within cross-scale composite microstructures. Considering in-situ compression and surface wettability, the research delves into the influence of MPL thickness and crack morphology on multiphase flow dynamics. The results indicate that despite the significant non-steady-state velocity fluctuations and reduced liquid permeability caused by cascading Haines jumps due to increased MPL thickness, its unique high-porosity cage-like network structure still maintains robust oxygen diffusion performance. In-situ compaction further weakens the macropore transport capacity of the gas diffusion layer (GDL), leading to a significant reduction in permeability. In contrast, fractures effectively break through transport bottlenecks. Vertical through-holes maximize oxygen diffusion efficiency through the shortest path effect, while 45 degrees inclined fractures optimize gas-liquid convective permeability while enabling directed high-speed drainage of liquid water. This study elucidates the regulation mechanism of microstructural parameters across scales, providing theoretical guidance for designing next-generation gas diffusion layers that combine high gas-phase diffusion with efficient drainage capabilities.