To investigate the influence of subgrade frost heaving deformation on track irregularity and structural stress, based on the ANSYS finite element analysis method and the research on the subgrade section of the frost heaving zone of the Harbin-Dalian high-speed railway, the spatial refinement finite element model of CRTS I type ballastless track was established by considering the characteristics of limit boss, gel resin, and interlayer contact. On this basis, effects of the locations of frost heaving deformation and different frost heaving wavelengths and amplitudes on the ballastless track structure were discussed, and the track irregularity, interface crack characteristics, and static performance were analyzed. Results show that under short-wave frost heave, indicators of irregularity, deformation, interface crack, and stress of the ballastless track structure increased with the decrease of the frost heaving wavelength and the increase of the frost heaving amplitude. When the frost heave occurred in the center of the baseplate, the stress on the track structure was the most affected, and when the frost heave occurred in the baseplate expansion joint, it had the greatest effect on the deformation and interface crack of the structure. Compared with the track slab, the baseplate bore the largest tensile stress, and the structural stress was more affected when the frost heave occurred in the center of the baseplate. In terms of the tensile strength of the ballastless track, the baseplate was the limited structure, and the frost heaving limiting values ware recommended to be 10 m for wavelength and 5 mm for amplitude.