To explore the dynamic transient characteristics induced by passing heavy-haul trains in newly-developed prestressed subgrade, two three-dimensional finite element models were constructed in the time domain using ABAQUS software. These models are categorized as train-track-prestressed subgrade and train-track-unreinforced subgrade. The numerical models also incorporated the vertical track irregularity commonly found in heavy-haul railways. The investigation aims to discern the dynamic stress response differences in both types of subgrades under three distinct train axle loads. Model validation occurred through comparisons with field tests gathered from various heavy-haul railways in China, as well as analogous numerical simulation cases. The findings indicate that track irregularity results in an asymmetric distribution of dynamic stress on the subgrade surface beneath both left and right rails, aligned transversely with the subgrade centerline. Additionally, this asymmetry is notably pronounced. The peak dynamic stress on the subgrade surface beneath the rails for both subgrades increases with escalating train axle loads. However, the prestressed reinforcement structure (PRS) effectively modulates this phenomenon, with the controlling advantage intensifying as train axle load increases. The average dynamic stress level in the prestressed subgrade is marginally lower than in the unreinforced subgrade within the roadbed layer beneath rails. Furthermore, train axle loads amplify the variation level of dynamic stress in the subgrade. However, the variable coefficient of dynamic stress in the prestressed subgrade is less than in the unreinforced subgrade, suggesting that PRS contributes positively to maintaining subgrade dynamic stability. In terms of the longitudinal distribution of peak dynamic stress, both subgrades exhibit normal distribution at varying depths within the roadbed layer. Lastly, the additional dynamic stress in prestressed steel bars also rises with increasing train axle loads. Nonetheless, it remains substantially lower than the static target pre-tensile stress. Moreover, the dynamic responses of prestressed steel bars in different rows attenuate as depth increases away from the subgrade surface. In summary, the study establishes that PRS significantly enhances the dynamic stability of railway subgrade.