Studying train-induced response characteristics is essential for safely operating permafrost railway subgrades. A three-dimensional thermal-mechanical coupling nonlinear dynamic model of train-track-subgrade-ground relationships was established to analyse the train-induced dynamic stress, acceleration and stress path characteristics of a permafrost railway subgrade, and field monitoring data were used to verify this model. The differences between the 2D and 3D models are also discussed, along with the seasonal changes, train speed, axle load, and train type affecting permafrost subgrades. The main results are as follows. First, the vibration load significantly impacts the subgrade 6 m below the sleeper, producing distinct vertical dynamic stress waves due to the wheels and bogies. Dynamic compression stress dominates the subgrade and is influenced by the train structure, speed, and sleeper spacing. While the 2D model tends to underestimate the dynamic stress in shallower layers, it concurs with the 3D model in deeper subgrade dynamics within a 10% margin of error. Then, the principal stress axis of the subgrade soil rotates synchronously with train movements, exhibiting regular stress paths in the YZ plane (longitudinal section) with depth-dependent variations in the stress cycles and deviatoric stress. Finally, predominantly originating from sleeper-induced vibrations, the subgrade vibration acceleration varies with the train speed, sleeper spacing, and season and is most pronounced in the vertical direction. This study provides theoretical guidance for the vibration response of permafrost subgrades on the Qinghai-Tibet Railway (QTR).