A microporous layer (MPL) with appropriate aperture and hydrophobicity is key for proton-exchange membrane fuel cells (PEMFCs). The MPLs are typically prepared from mixing carbon black and a hydrophobic agent (i.e., polytetrafluoroethylene) physically followed by annealing at elevated temperatures, resulting in pore blockage and carbon black aggregation. To address this issue, we report a facile method to fabricate uniform porous carbons (UPCs) with single aperture and hierarchical porous carbon (HPC) with multiple apertures using a hard silica template followed by chemical grafting with hydrophobic fluoroalkylsilane (FAS-17). An advanced MPL (GMPL) is fabricated by direct layer-by-layer construction of hydrophobic UPC with different apertures, demonstrating improved water drainage and efficient gas transportation, thereby delivering high output power density of 809.64 mW·cm−2. The as-fabricated GMPL demonstrates superior performance as compared to the one containing MPL prepared with HPC (HPC-MPL, 781.20 mW·cm−2) and the ones employing MPL with a single aperture (714.38–749.89 mW·cm−2). The controllable gradient aperture, superhydrophobicity, and open pore/channels contribute to the high performance of PFMFC. This work presents a feasible structural design for MPLs toward high-performance PEMFC. [ABSTRACT FROM AUTHOR]