During all the assembly stages of a polymer electrolyte membrane fuel cell (PEMFC) stack, gas diffusion layers (GDLs) endure clamping loads in the through-plane direction several times. Under such complicated assembly conditions, GDLs have to deform with the changes in structure, surface roughness, pore size, etc. A comprehensive understanding of the compressive performance of GDLs at different clamping phases is crucial to the assembly process improvement of PEMFCs. Two typical clamping compression was designed and performed to get close to the actual assembly conditions of PEMFCs. The results indicate that the initial clamping compression and the magnitude of the maximum clamping load have great impacts on the segmented compressive properties of GDLs. The nonlinear compressive performance of the GDL is mainly attributed to the unique microstructural information. The rough surface morphology contributes to the initial compressive characteristics where the big strain along with the small stress occurs, and the irreversible failures such as carbon fiber breakages and adhesive failures between fibers and binders account for the hysteresis between different compression stages. Importantly, it is found that the clamping compression hardly influences the small pore distribution below 175 μm but affects the large pore distribution over 200 μm.