In order to understand the hydrothermal activity mechanism of active layers to rainfall in permafrost regions caused by humidification of climate, the differences of ground surface energy balance and hydrothermal activity in different types of shallow soil with the consideration of rainfall were discussed. Based on the meteorological data in 2013 observed at Beiluhe observation station of Tibet Plateau, three types of shallow ground soil (i.e., sandy soil, sandy loam and silty clay) were selected to compare the differences in the water content and energy balance at the ground surface, dynamic processes of water and energy transport in active layers and coupling mechanism under rainfall condition in the plateau using a coupled water-vapor-heat transport model. The results show that the increase of soil particle size leads to the increase of surface net radiation and latent heat of evaporation, but the decrease of soil heat flux. The difference of surface energy balance, especially the sensible heat flux and latent heat of evaporation, are larger in the warm season but smaller in the cold season. The liquid water transport under hydraulic gradient and the water-vapor transport under thermal gradient are obvious as the particle size in soil increases. However, the water-vapor flux under thermal gradient increases but the liquid water flux under hydraulic potential gradient decreases. As a result, the water content in shallow soil decreases accordingly but it increases slightly at the depth of 25~–75 cm. Moreover, with the increase of soil particle size, the thermal conductivity of soil, convective heat transfer under rainfall and surface evaporation increase, but the soil heat conduction flux and soil temperature gradient decrease. Thus, soil temperature in sandy soil is much higher than that of sandy loam and silty clay at the same depth. The permafrost table declines with the increase of the thickness of active layer, which is unfavourable to permafrost stability. The results can provide theoretical reference for stability prediction and protection of permafrost caused by humidification of climate.