Proton exchange membranes with high through-plane proton conductivity are a critical component of high-performance fuel cells, electrolyzers, and batteries. However, isotropically distributed proton-conducting channel structures of current membranes present a limitation. Herein, a proton exchange membrane with straight proton-conducting channels aligned in the thickness direction is fabricated, achieved by magnetic field-induced alignment of proton-conductive, paramagnetic, and one-dimensional (1D) tungsten disulfide nanotubes (pms-WS2) distributed in a perfluorinated sulfonic acid (Nafion) membrane. The pms-WS2 nanotubes feature straight WS2 nanotubes as a core, a polystyrenesulfonate (PSS) skin layer, and surface-decorated Fe3O4 nanoparticles. A molecular dynamics simulation suggests that straight proton-conducting channels are constructed at the interface of Nafion/pms-WS2 due to densely populated sulfonic acids. Spectroscopic investigation and magnetization measurements verify the through-plane alignment of pms-WS2 under a weak through-plane magnetic field (0.035 T) during the removal of solvent from the membrane cast. Compared with a recast Nafion membrane with the same thickness, the through-plane aligned composite membrane exhibits 69% higher proton conductivity and 51% higher power performance in a proton exchange membrane fuel cell, demonstrating its efficacy. The through-plane alignment of a proton-conductive inorganic 1D material promises improved power performance of advanced electrochemical devices.