Designing an efficient and reliable tritium plant has become a major challenge to developing nuclear fusion, which focuses on efficient and safe hydrogen isotope separation and purification. The electrochemical hydrogen pump (EHP) developed in recent years can be used to separate and compress hydrogen. Herein, we used the commercial Nafion membrane electrode in the EHP, which has excellent H2/CH4 separation performance. When the cell voltage is at 0.8 V, the current density is 2.04 A/cm2, the hydrogen separation rate can reach 14.2 mL/ (min ·cm2), and the hydrogen purity is more than 99.99 %. The damage mechanism of electron beam irradiation on the membrane electrode was revealed. It was found that irradiation caused Nafion’s main chain and branch chain to break, producing hydroxyl and carboxyl functional groups. The degree of chain fracture increased with the radiation dose, perforation and cracks occurred in the proton exchange membrane (PEM). Under the electron beam irradiation dose of 10 kGy, the membrane electrode can still maintain excellent H2/CH4 separation performance, and the hydrogen permeability caused by cracks and perforations is at a very low level. This study reveals the change of macroscopic performance caused by the microscopic mechanism of membrane electrode irradiation damage, provides a promising way to separate hydrogen isotope gases and is expected to promote the development of tritium plants in fusion engineering.