Abstract: Proton exchange membrane (PEM) water electrolysis presents a blueprint for high-efficiency green hydrogen production. However, hydrogen (H₂) permeation across the PEM poses challenges to the efficiency and safety of PEM water electrolysis. Herein, we investigated the hydrogen permeation process on the prepared perfluorinated sulfonic acid (PFSA) membrane with a thickness range from 50 μm to 180 μm, demonstrating the influence mechanism of PEM structure on hydrogen permeation. Five kinds of perfluorinated sulfonic acid PEM with different thickness were cast from Nafion D520 dispersion into quartz vessels. Membrane electrode assembly (MEA) was assembled into a single cell by a hot press transfer method. Electrochemical tests and gas chromatography were used to validate the influence of the thickness of PEM on the cell performance and H₂ permeation of PEM water electrolysis. The permeation of H₂ is not simply inversely proportional to the thickness of the films, which may be due to structural differences between films. To further elucidate the modulating mechanism of PEM structure on H₂ permeation, the relative crystallinity of the membrane and the mean spacing between the hydrophilic water-domains were tested through X-ray diffraction and scattering experiments. Additionally, grey correlation analysis (a mathematical statistical analysis method) was performed on the collected data. The analysis revealed the prominent modulating effect of the membrane structure parameters (water content (S), crystallinity (X_c) and water-domains spacing (D_w) on the H₂ permeation, with D_w identified as the primary factor affecting H₂ permeation. These parameters influence the size and connectivity of the hydrophilic water-domains within the membrane impacting the size and length of the H₂ diffusion path and resulting in differences in hydrogen diffusion rate. This study aimed to investigate the influence mechanism of proton exchange membrane structure on hydrogen permeation, offering fresh perspectives on research into the hydrogen permeation performance of proton exchange membranes. Our study offers a guidance for researchers in the development of cost-effective and secure membranes for use in PEM water electrolysis.