Abstract In this study, a whole-cell 3D multiphase non-isothermal model is developed for hydrogen alkaline anion exchange membrane (AAEM) fuel cell, and the interfacial effect on the two-phase transport in porous electrode is also considered in the model. The results show that the insertion of anode MPL, slight anode pressurization and reduction of membrane thickness generally improve the cell performance because the water transport from anode to cathode is enhanced, which favors both the mass transport and membrane hydration. The effect of cathode MPL is generally insignificant because liquid water rarely presents in cathode. It is demonstrated that slight pressurization of anode, which might not lead to apparent damage to the membrane, can effectively solve the anode flooding and cathode dryout issues.