Non-precious metal M-N-C catalysts have a low density of active sites, which requires increasing the catalyst loading amount per unit area to obtain sufficient active sites to ensure the required apparent output current of the proton exchange membrane fuel cells (PEMFCs). This inevitably increases the thickness of the catalytic layer. On the one hand, a thick catalytic layer increases the resistance to material transfer, and on the other hand, a thick catalytic layer is more prone to causing “flooding” problems, which further worsens the material transfer problem of the catalytic layer. To address the water flooding and material transfer efficiency challenges of Fe-N-C cathode catalytic layers, this study employed controlled pyrolysis of perfluorinated sulfonic acid ionomer side chains with hydrophilic sulfonic acid groups within the catalytic layer. The in-situ modulation of the hydrophilic-hydrophobic balance at the active sites of the catalyst creates an efficient three-phase interface, enabling high ion conductivity and efficient water and oxygen transport within the Fe-N-C catalytic layer. Consequently, the output performance and stability of the membrane electrode are significantly improved. The results demonstrate that the degree of sulfonic acid group pyrolysis within the catalytic layer ionomer can be effectively controlled by adjusting the pyrolysis temperature and duration. Using a catalytic layer with an ionomer to Fe-N-C catalyst mass ratio (I/C) of 0.5 as a model, the perfluorinated sulfonic acid ionomer's sulfonic acid group decomposition rate was 16.3% after 40 minutes of heat treatment at 250 ℃ under a N₂ atmosphere, resulting in an increased hydrophobicity of the catalytic layer surface, as indicated by a surface water contact angle increasing from 113° to 134° while maintaining high ion conductivity. The corresponding membrane electrode exhibited optimal output performance, with a peak power density of 359.7 mW• cm^－2, representing a 38% improvement over the pre-treatment electrode. Additionally, under a constant voltage of 0.4 V, the material transfer resistance of the heat-treated catalytic layer decreased by 29.8% to 242.48 mΩ•cm² compared to the pre-treatment condition. During the 20-hour constant voltage discharge test at 0.4 V, the heat-treated Fe-N-C catalytic layer exhibited higher discharge current density than the untreated membrane electrode. This study demonstrates that partially controlled pyrolysis of catalytic layer ionomer is an effective method for improving the performance and stability of M-N-C non-precious metal catalyst membrane electrode fuel cells.