Fractal characteristics of interface micro-porous structure is studied in detail with three-dimensional numerical reconstruction technology of fractal rough surface. An interfacial leakage mechanism model is built based on fractal porous media transport theory. Relation between microscopic morphology and macroscopic leakage rate is obtained. Contact behavior of a single asperity is simulated with finite element analysis, and deformation displacement of the maximum aperture is obtained. Effective coupling between microscopic contact mechanics and microscopic leakage model is achieved. Results of prediction model are in good agreement with experimental results in predicting metal gasket leakage rate. It is found that fractal dimension, and characteristic scale coefficient of rough surface and deformation displacement have great influence on geometry morphology of interface microporous structure, and therefore, are key factors of interfacial leakage rate.