In the paper, a gas diffusion layer with a stacked microporous layer structure was prepared using three different conductive materials. The new gas diffusion layer mainly consisted of a gas diffusion backing layer and a stacked microporous layer. The stacked microporous layer was composed of conductive carbon black materials with different particle sizes, and the purpose was to change the capillary pressure difference within the microporous layer to improve the water–gas management capability of the gas diffusion layer, and to explore the effect of the change in the pore structure of the gas diffusion layer on the water–gas management capability of the proton exchange membrane fuel cell. The results showed that the design of the stacked microporous layer realized the redistribution of gas diffusion layer apertures, and the number of 7–20 μm apertures and 20–50 μm apertures conducive to water and gas transfer increased, which improved the substance transfer capability of the single-cell at high current density. The sample with the best performance, GDL-C, had the most reasonable capillary pressure difference distribution, which prompted liquid water and gas to exchange substances in the fuel cell under the effect of a gradient capillary pressure difference, thus improving the output performance of the fuel cell. Under the hydrogen-air test environment, the limiting power density of sample GDL-C reached 0.754, 0.818, and 0.731 W cm⁻2 under low, medium, and high humidity conditions, respectively, which was an excellent performance. Graphical abstract: (Figure presented.) © The Author(s), under exclusive licence to Springer Nature B.V. 2024.