In this paper, we report the preparation of a gas diffusion layer (GDL) with different gradient pore size structures. The pore structure of microporous layers (MPL) was controlled by the amount of pore-making agent sodium bicarbonate (NaHCO3). We investigated the effects of the two-stage MPL and the different pore size structures in the two-stage MPL on the performance of proton exchange membrane fuel cells (PEMFC). The conductivity and water contact angle tests showed that the GDL had outstanding conductivity and good hydrophobicity. The results of the pore size distribution test indicated that introducing a pore-making agent altered the pore size distribution of the GDL and increased the capillary pressure difference within the GDL. Specifically, there was an increase in pore size within the 7–20 μm and 20–50 μm ranges, which improved the stability of water and gas transmission within the fuel cell. The maximum power density of the GDL03 was increased by 37.1% at 40% humidity, 38.9% at 60% humidity, and 36.5% at 100% humidity when compared to the commercial GDL29BC in a hydrogen-air environment. The design of gradient MPL ensured that the pore size between carbon paper and MPL changed from an initially abrupt state to a smooth transition state, which significantly improved the water and gas management capabilities of PEMFC.