The interface leaking of the gasket-BPP sealing structure affects the efficiency, safety, and reliability of PEMFCs. Aiming to reveal the basic cause of interface leaking and predict the leakage rate, the contact behavior at the micro-scale had been researched by FEM with the fractal multi-scale method, which could eliminate the negative influence of a single observation scale on the gasket-BPP rough interface modeling. Furthermore, in order to relate the contacting behavior at the micro-scale to the leakage rate at the macro-scale of PEMFCs, the mapping model had been established to analyze the sealing performance of the entire interface through the self-affine and self-similar characteristics of the fractal multi-scale contacting model of the gasket-BPP. Not only macroscopic properties of gasket rubber materials are considered in this model, but also microscopic morphologies are taken in to investigate the interface leakage rate, which had not been studied in traditional macroscopic research. By comparing the compression curves and interface leakage rates of the flange sealing device in testing and calculating approaches, the accuracy and reliability of the mapping model had been verified, leading to the analysis and the prediction of the PEMFC interface leakage rate rapidly.