The canopy effect refers to the effect that road surfaces or other surface coverings have when they block the water evaporation from subgrade soil, causing moisture accumulation underneath the road surface. For railway subgrades, evaporation is not completely blocked by the stone ballast layer. When shallow soil gradually freezes in winter, the top cover effect becomes stronger. This effect is called the canopy effect with time-varying top boundary conditions. Numerical simulation of this kind of canopy effect is important to the control of frost heaving of railway subgrades. In this paper, the previously presented canopy effect model is extended by considering the top boundary variation in addition to unsaturated soil moisture migration and frost heave formulation. Moreover, it is clarified that an ice-water-air multiphase zone exists during the development of this kind of canopy effect. Consideration of the interaction and development process of each phase in this multiphase zone is necessary for accurate analysis of this kind of canopy effect. Water migration, the thickness of the ice-water-air multiphase zone and the development of frost heave in the subgrade soil under different initial volumetric water contents or temperature differences are analyzed to demonstrate the applicability of the proposed mathematic model.