Abstract The traditional perfluorosulfonic acid proton exchange membrane is crucial for proton exchange membrane fuel cells, but its high cost has impeded broader commercialization. In this study, a novel concept of a cost‐effective and stable vertically aligned polydopamine‐intercalated montmorillonite membrane (VAPMM) is introduced. 2D nanochannels formed within the lamellar structure of polydopamine‐coated montmorillonite nanosheets provide a significant stable in‐plane proton conductivity of 0.58 S cm −1 . The stacked lamellar structure is embedded in epoxy resin to maintain its orientation. Subsequently, precise slicing along the vertical direction of the 2D nanochannels yields a thin film ≈150 µm thick, featuring vertically aligned proton conductive transmembrane nanochannels. When assembled into a membrane electrode assembly with commercial gas diffusion electrodes, the VAPMM exhibits a maximum areal peak power density of up to 534.00 mW cm −2 at 75 °C with 100% RH, surpassing by more than four times that of a commercial Nafion membrane of similar thickness (N117, 183 µm, 116.17 mW cm −2 ). This study outlines a pathway for developing next‐generation proton exchange membranes that are both cost‐effective and highly stable. Additionally, it introduces a straightforward method to create fully vertically aligned transmembrane nanochannels while preserving the interlayer structure, which is crucial for advancements in nanofluidics.