An acceleration stress test (AST) was performed to evaluate the durability of a polymer membrane in a polymer electrolyte membrane fuel cell (PEMFC) for 500 hours. Previous studies have shown that hydrogen crossover measured by linear sweep voltammetry (LSV) increases when the polymer membrane deteriorates in the AST process. On the other hand, hydrogen crossover of the membrane often decreases in the early stages of the AST test. To investigate the cause of this phenomenon, we analyzed the MEA operated for 50 hours using the AST method (OCV, RH 30% and 90 °C). Cyclic voltammetry and transmission electron showed that the electrochemical surface area (ECSA) decreased due to the growth of electrode catalyst particles and that the hydrogen crossover current density measured by LSV could be reduced. Fourier transform infrared spectroscopy and thermogravimetric/differential thermal analysis showed that -S-O-S- crosslinking occurred in the polymer after the 50 hour AST. Gas chromatography showed that the hydrogen permeability was decreased by -S-O-S- crosslinking. The reduction of the hydrogen crossover current density measured by LSV in the early stages of AST could be caused by both reduction of the electrochemical surface area of the electrode catalyst and -S-O-S- crosslinking.