The proton exchange membrane (PEM) fuel cell is a clean power generation component with high energy conversion rate and high energy density. The triple-phase interfaces of catalytic layer are where the electrochemical reaction occurs in proton exchange membrane (PEM) fuel cell, and its distribution directly affect the reactivity. The triple-phase interface is a nano-thick perfluorosul-fonic acid ionomer (PFSA) film that covers the catalyst particles. When the density of the ultra-thin PFSA film is not uniform, the gas transport resistance increases significantly, which is not conducive to the progress of reaction. However, ultra-thin PFSA film will have inhomogeneous density distribution due to the influence of forming process. Therefore, how to design the process to improve density distribution of ultra-thin films is an urgent problem. Molecular dynamics simulation model is built to study the influence of manufacturing process on inhomogeneous distribution of ultra-thin PFSA film, and the microscopic mechanism is revealed.