Abstract Harmonic excitation can significantly increase the dynamic response of wheel-rail interactions when a train passes. In this study, based on the train-track vertical coupled dynamics model (ZL-TNTLM) and ABAQUS, a unified train-track-subgrade coupled dynamics model is established. Field measurement data corroborated its accuracy and reliability. The analysis focused on the dynamic response of the permafrost subgrade of the Qinghai-Tibet Railway (QTR) to harmonic excitation, including the track-sleeper force and vertical dynamic stress. This study examined the influences of the wavelength, wave depth, and railhead depression on the dynamic response of a subgrade. The results indicated that single-harmonic excitation amplifies the track-sleeper forces and the vertical dynamic stress in the subgrade, particularly near the harmonic centre. Additionally, axle load variations and seasonal thawing broaden the dynamic stress range on the subgrade, with harmonic excitation exacerbating this impact, thereby increasing the risk to the stability of the ice-rich permafrost layer. A decrease in wavelength and increase in wave depth result in a greater number of affected sleepers, intensifying the vertical vibrations of the subgrade, especially in the medium- and high-frequency ranges of vertical dynamic stress. Notably, wavelengths between 1 and 2 m significantly exacerbate the adverse effects on the ice-rich permafrost layer. Shorter wavelengths also induce higher-frequency vibrations. These findings offer valuable insights for the design, operation, and maintenance of permafrost subgrade systems under irregular excitation.