The performance of the sealing is closely related to the working efficiency and safety of PEMFCs and the interfacial leaking behavior is heavily influenced by the heterogeneous rough surfaces. And the BPPs and Gaskets of the fuel cell sealing structure are ultra-thin, which makes obtaining leakage rate by experiments difficult. In this paper, a highly efficient method to calculate the PEMFC sealing interface leakage rate is proposed based on the fractal geometry and numerical simulations. FEM and LBM methods are used to analyze the nonlinear contact and microscopic gas flow behaviors in the numerical simulation processes. Furthermore, a multi-scale dimensionless model of PEMFC interface leaking is established by numerical simulated results. The multi-scale dimensionless model can significantly reduce the negative influence of the single observation scale on interface leakage rate prediction accuracy and solve the problem of the inability to analyze interface leakage rates at different scales simultaneously. By comparison with the Roth's theory, the traditional model that only considers the small elastic deformation has a large deviation in the evaluation of the leakage rate of the rubber seal interface, while the multi-scale model can accurately predict the interface leakage rate under different PEMFC Gasket compression rates.