In the context of global warming, the precipitation in the Tibetan Plateau region keeps increasing. Excessive rainfall contributes to the change of the moisture boundary, so it is necessary to explore the influence of moisture boundary on the hydrothermal process of permafrost embankments. Based on the theory of thermal conduction and seepage in unsaturated soils, this study established a coupled hydrothermal model of permafrost embankments considering moisture migration and phase change. Subsequently, a moisture boundary integrating rainfall and evaporation was introduced into the numerical model. The simulation results of water content, temperature, and fluxes by the model were then compared with those by the model without a moisture boundary. The results show that neglecting the moisture boundary in the warm season will underestimate the water content and overestimate the soil temperature. After introducing the moisture boundary, the shallow liquid water content of the embankment fluctuates in the range of 0.06-0.11 m3/m3 in the warm season, which can increase up to 36.14% compared with that without a moisture boundary. Rainwater sensible heat and evaporative latent heat redistribute the surface energy, so that the thermal conduction flux decreases, resulting in a maximum temperature drop of 0.75 ℃ in the average temperature of the embankment shallow layer in the warm season compared with that without a moisture boundary.