This paper studies the performance of a nonlinear anisotropic turbulence model developed in the basis of a statistical partial average scheme. The first order velocity of turbulent fluctuations, retained by a novel average scheme, and turbulent length scale can be determined from the momentum equations and mechanical energy equation of the fluctuation flow, respectively. The two physical quantities are readily to construct the nonlinear anisotropic eddy viscosity tensor and to significantly improve computational results. Two typical shock-wave-boundary-layer-interaction (SWBLI) separation flows are deeply studied using CFD method. One is an incident oblique shock wave impinging on a flat plate with a turbulent boundary layer, and the other one is a transonic turbulent separation flow in a converging-diverging transonic diffuser. Comparisons between the computational results and experimental data are carried out for velocity profiles, density contours, pressure distribution, skin friction coefficient, Reynolds stress as well as streamline vectors distribution. Without using any empirical coefficients and wall functions, the numerical results are in good agreement with the available experimental data, which further confirms that the nonlinear anisotropic eddy viscosity tensor is of the decisive factor for the success of the computational results.