Gas diffusion layers (GDLs) are critical to optimizing water management capability; however, carbon papers (CPs), as the substrates that provide channels for two-phase counter flows of reactant gases and product water, have rarely been reported for controlling product water. In this study, gradient pore structures were introduced into CPs for GDLs to control the driving forces of water using the capillary pressure gradient. The results showed that the gradual increase in the pore sizes of the CPs from the microporous layer (MPL) to the bipolar plate (BP) side significantly improved the electrochemical performance, regardless of humidity. At 100 % relative humidity (RH), the maximum power density of the membrane electrode assembly (MEA) whose CP pore sizes gradually increased from the MPL side to the BP side reached 1.78 W·cm−2 under H2-O2 condition, 40.16 % higher than that of the counterpart with uniform CP pore sizes, and 1.28 W·cm−2 under H2-air condition, 85.51 % higher than that with uniform CP pore sizes. The maximum current density increases under both wet and dry conditions. The mechanisms revealed that under dry conditions, the relatively smaller pores in the CPs close to the MPL side enhanced the water retention and thus maintained the proton conductivity; under wet conditions, the CP pores that were gradually enlarged from the MPL to the BP side enabled the capillary pressure gradient to guide the product water from the MPL flowing into and through the CP, and thus out of the GDLs.