To examine the influence of polygonal wheels on the dynamic responses of high-speed train, a vehicle-track dynamics model was developed. This model incorporated gear transmissions using multibody dynamics methodology and gear dynamics theory. The effect of gear transmissions on the dynamic responses of the high-speed train was evaluated by comparing the results of the developed model with those of a non-geared traditional model. The dynamic responses of the train were studied by examining the combined effects of wheel polygonal excitation and time-varying mesh stiffness excitation. The results indicated that the vertical wheel-rail contact force and vibration amplitude of the model with polygonal wheels were larger than those of the normal model. Similarly, the geared transmission model exhibited greater contact force and vibration amplitude compared to the non-geared transmission model, attributed to the increased excitation. The evolution of the wheel polygon’s order and wear depth could significantly increase the vertical wheel-rail contact force and the wheel load reduction rate. The safety limits for wheel polygon order and wear depth were established. The model with gear transmissions is more closely aligned with the actual situation and exhibits higher safety performance, providing valuable reference for wheel turning.