The excellent microporous layers (MPLs) in the gas diffusion layer requires superior mass transfer capacity, which is essential to high-performance proton exchange membrane fuel cells. However, the correspondence between MPL structure and mass transfer performance is ambiguous. Here, we design efficient mass transfer channels in MPLs with evolutionary structures by adjusting the content of whisker-like carbon nanotubes (WCNTs). The cell power density exhibits a bimodal shape with the increase of WCNTs in MPLs, which verifies that the perforated cracks of 5–10 μm in the MPL provide the separated channels for water and gas transport, and the optimal hydrophobic mesopores (34.87%) promote the mass transfer efficiency by elevating the capillary force of water transport. At 100% relative humidity (RH), the peak power densities of cells with the two MPLs are increased to 2.321 W cm−2 and 2.117 W cm−2, respectively. The electrochemical impedance spectroscopy confirms that the impedance of both MPLs are 109.35 mΩ cm2 and 63.55 mΩ cm2 at 100% RH and 3 A cm−2. The simple and scalable strategy provides a novel idea to relieve the mass transport loss of fuel cells.