Gear geometric eccentricity is a common and unavoidable manufacturing error form that the mass center does not coincide with the geometric center, which mainly stems from the manufacturing and assembly processes. The gear geometric eccentricity will exert the considerable effect on the time-varying mesh stiffness excitation and cause the error excitation, which will further induce the abnormal vibration, impact, noise of the gear transmission system especially under the complex excitations from wheel and rail interface. The dynamic behaviors of the gear transmission system in complex vibration environment will be complex and need to be revealed. In this paper, the dynamic analysis model of the high-speed train-track coupled system is established considering the gear geometric eccentricity. Furtherly, the effects of the different eccentricity of the driving gear and driven gear on the dynamic features of the gear transmission system from the perspective of the time history and frequency spectrum are analyzed. This study can give some theoretical reference for the manufacturing process of the gear pair.