In order to find out the influence of subgrade frost heave on the deformation of track structure and track irregularity of high-speed railways, a nonlinear damage finite element model for China Railway Track System III (CRTSIII) slab track subgrade was established based on the constitutive theory of concrete plastic damage. The analysis of track structure deformation under different subgrade frost heave conditions was focused on, and amplitude the limit of subgrade frost heave was put forward according to the characteristics of interlayer seams. This work is expected to provide guidance for design and construction. Subgrade frost heave was found to cause cosine-type irregularities of rails and the interlayer seams in the track structure, and the displacement in lower foundation mapping to rail surfaces increased. When frost heave occured in the middle part of the track slab, it caused the greatest amount of track irregularity, resulting in a longer and higher seam. Along with the increase in frost heave amplitude, the length of the seam increased linearly whilst its height increased nonlinearly. When the frost heave amplitude reached 35 mm, cracks appeared along the transverse direction of the upper concrete surface on the base plate due to plastic damage; consequently, the base plate started to bend, which reduced interlayer seams. Based on the critical value of track structures’ interlayer seams under different frost heave conditions, four control limits of subgrade frost heave at different levels of frost heave amplitude/wavelength were obtained.