In this study, a nonlinear dynamic model of a spur gear transmission system with non-uniform wear is proposed to analyze the interaction between surface wear and nonlinear dynamic characteristics. A quasi-static non-uniform wear model is presented, with consideration of the effects of operating time on mesh stiffness and gear backlash. Furthermore, a nonlinear dynamic model with six degrees-of-freedom is established considering surface friction, time-varying gear backlash, time-varying mesh stiffness, and eccentricity, and the Runge–Kutta method applied to solve this model. The bifurcation and chaos in the proposed dynamic model with the change of the operating time and the excitation frequency are investigated by bifurcation and spectrum waterfall diagrams to analyze the bifurcation characteristics and the dimensionless mesh force. It is found that surface wear is generated with a change in operating time and affects the nonlinear dynamic characteristics of the spur gear system. This study provides a better understanding of nonlinear dynamic characteristics of gear transmission systems operating under actual conditions.