In order to accurately and effectively obtain the contact performance of the mating surface under the material surface topography characteristics, a numerical simulation method of rough surface based on the real topography characteristics and a multi-scale hierarchical algorithm of contact performance is studied in this paper. Firstly, the surface topography information of materials processed by different methods was obtained and characterized by a measuring equipment; Secondly, a non-Gaussian model considering kurtosis and skewness was established by Johnson transform based on Gaussian theory, and a rough surface digital simulation method based on real surface topography was formed; Thirdly, a multi-scale hierarchical algorithm is given to calculate the contact performance of different mating surfaces; Finally, taking the aeroengine rotor as the object, the non-Gaussian simulation method was used to simulate the mating surfaces with different topographies, and the multi-scale hierarchical algorithm was used to calculate the contact performance of different mating surfaces. Analysis results showed that the normal contact stiffness and elastic–plastic contact area between the mating surfaces of assembly 1 and assembly 2 are quite different, which further verifies the feasibility of the method. The contents of this paper allow to perform the fast and effective calculation of the mechanical properties of the mating surface, and provide a certain analysis basis for improving the surface microtopography characteristics of materials and the product performance.