Surface topography of sealing interface is a key factor affecting sealing performance. In industry, it has always been desirable to optimize the performance of static seals by optimizing the surface topography. The evolution of leak channels and the quantitative effects of surface topography on leak rates are expected to be clarified. This paper proposes a novel approach to calculate leak channels and leak rates between sealing surfaces for specific surface topographies, based on three-dimensional (3D) finite-element contact analysis. First, a macromechanical analysis of the entire sealing structure is conducted to calculate the interfacial pressure. Second, the surface topography data are measured and processed. Third, the interfacial pressure is used as the boundary condition applied on the microscale 3D finite-element contact model, which is built based on the specific surface topography. Fourth, the geometrical models of leak channels are extracted from the finite-element contact model, and the leak rates are calculated using the computational fluid dynamics (CFD) method. The proposed approach was applied to a hollow bolt-sealing structure. Finally, experimental results verified the accuracy and effectiveness of the proposed approach, which can provide valuable information for optimizing surface processing techniques, surface topography, and static seal performance.