Abstract: In order to study the influence of running-in on the tooth surface morphology and vibration characteristics of the variable angle reducer, firstly, the fractal parameters of the tooth surface after running-in were calculated by using the structure function method, and the actual rough tooth surface morphology was simulated by combining the fractal theory and the gear involute equation. Secondly, a dynamic model of bevel gear-rotor-bearing with 16 degrees of freedom was established, which takes into account tooth surface morphology and time-varying meshing stiffness. Thirdly, the time-varying meshing stiffness was calculated by the potential energy method combined with the distribution function of the micro-convex body, and the time-varying meshing stiffness change before and after running-in was analyzed, the fractal function was used to construct the rough meshing gap of the gear. Finally, the Runge-Kuta numerical integration method was used to solve the model, and the vibration characteristics of the system before and after running-in were compared by experiments. The results show that the fractal parameters calculated by the structure function method can effectively simulate the microscopic tooth surface morphology of the variable angle reducers. The running-in process significantly changes the shape of the tooth surface, reduces the roughness of the tooth surface and the meshing clearance of the gear, and reduces the time-varying meshing stiffness. With the reduction of tooth surface roughness, the amplitude of meshing frequency of the system decreases obviously, and the vibration characteristics are improved significantly. The experimental results are in good agreement with the theoretical analysis, which provides a theoretical basis for the study of running-in technology of variable angle reducers.