Gears are important components of the transmission system. Tooth wear and bearing clearance are significant factors affecting the dynamics of the gear system. In order to reveal the effects of gradual wears and bearing clearance on the gear system dynamics, a six-degrees-of-freedom bending-torsion coupled model of gear-rotor-bearing which considers surface wear, bearing clearance and backlash is established. The Rung-Kutta method is used to solve the nonlinear dynamic system, and the dynamic responses of the system are obtained. The results show that the time-varying mesh stiffness decreases with the tooth surface from the unworn phase to severe wear phase. At the same time, the change of the mesh stiffness in the double-tooth mesh area and single-tooth area are different. Moreover, the amplitude of the X-displacement, Y-displacement and relative gear mesh displacement will be enlarged slightly with the increase of wear depth or bearing clearance. By analyzing variation tendency in the frequency domain, the different order harmonics show the different change characteristic with the variation of the wear phases or bearing clearances. This study provides a theoretical basis for improving the transmission performance and the selection of the bearing clearances in the gear system.