By using the transient finite element method, a three-dimensional wheelset-track coupled rolling contact model for high-speed rail is established, and the rationality and effectiveness of the model are verified by field measurements. Next, the wheel-rail contact stress states and relative slip characteristics are calculated and analyzed to reveal the cause of inner rail corrugation. Then, the vertical vibration acceleration of the rail/wheel is taken as the output variable to study the dynamic responses of the wheelset-track system. Finally, the parameter sensitivity analysis is carried out. The results show that the maximum normal/tangential contact stress between the inner wheel and inner rail is greater than that between outer wheel and outer rail due to the unbalanced load of inner rail caused by the excess superelevation of track structure, which indicates that the unbalanced load of the inner rail may aggravate the development of rail wear, and the rationality of the model established in this paper is verified. The wheel-rail relative slip region on the inner rail side appears periodically, and the distance between the two adjacent slip regions is close to the characteristic wavelength of the measured inner rail corrugation, which illustrates that the periodic variation of slip regions on the inner rail surface plays an important role in the formation of rail corrugation, and the validity of the model is verified. The periodic distribution of wheel-rail relative slip regions on the outer rail surface is not obvious, demonstrating that the outer rail tends to form uniform wear, which is consistent with the fact that the outer rail corrugation is slight in the measured section. The wheelset-track system has been in the process of unstable continuous oscillation in the analysis interval, combined with the analysis results of the wheel-rail relative slip characteristics, it can be concluded that the unstable self-excited vibration of wheelset-track system under the condition of tangential contact force reaching saturation is the main cause of rail corrugation. The dominant characteristic frequencies of vertical vibration accelerations of rail and wheel are all 561 Hz, the corresponding characteristic wavelength (148 mm) is close to the distance (150 mm) between the calculated adjacent slip regions, and is also close to the characteristic wavelengths (125 mm and 160 mm) of inner rail corrugation, which shows that the resonance phenomenon occurs in the wheelset-track system at the above frequency, thus leading to the increase of dynamic responses of wheelset-track system. The fastener vertical stiffness and wheel-rail coefficient of friction have significant effect on the development of rail corrugation, and the running speed determines the occurrence probability of inner/outer rail corrugation by affecting the track superelevation state.