Based on the theory of vehicle track coupling dynamics, through the finite element analysis of the coupling system model of high-speed train-ballastless track-subgrade, this paper studies the dynamic influence of uneven frost heave of high-speed railway subgrade on the train and track, analyzes the system vibration response law caused by frost heave deformation under different conditions, and then puts forward relevant improvement measures to facilitate the benign development of the system. The results show that the uneven frost heaving of the subgrade will cause the dynamic response of the train and the track, reduce the service performance of the track structure, and is not conducive to the traffic safety. In the typical case of frost heaving, when the train enters into the frost heaving area, the impact caused by the vibration at the initial position is relatively large; with the increase of the frost heaving wavelength of the subgrade, the impact on the vibration of the vehicle body decreases successively, while the impact of the frost heaving peak is the opposite. The improvement of frost heave in the range of 25m, especially in the range of 10m to 15m, can enhance the driving safety and riding comfort. At the same time, focusing on controlling the peak value of Subgrade Frost Heaving can effectively reduce the fatigue damage of track structure.