Abstract: The research on the mechanism of hydrothermal transfer and transformation and bare soil evaporation is of great significance for water balance and surface energy transformation in surface-groundwater systems. In this paper, based on long-term observations of in situ lysimeter test and numerical simulation, two cases for lysimeter with initial groundwater depths of 80 cm (shallow groundwater depth) and 290 cm (deep groundwater depth) are used to examine the dynamic process of hydrothermal transformation in the variable saturation zone with its effect on bare soil evaporation in the “wind-blown sand area” of the Ordos Basin in China. The results indicate that soil water movement in the variable saturation zone is driven by the head gradient and temperature gradient, showing different movement modes under different groundwater depths. For the situation of shallow groundwater depth, the capillary height can reach the surface, soil water transports upwards with little temperature effects driven by capillary force under the effects of head gradient under the evaporation conditions, and there is no zero flux plane in the soil. When the groundwater depth is less than the capillary height, groundwater directly contributes to soil evaporation driven by capillary force. For the situation of deep groundwater depth, head and temperature are the key factors in the soil water movement, and there is an isolated zero flux plane located at 18 cm below the ground surface, which prevents the upward soil water movement and leads to a decrease in evaporation. When the groundwater depth is greater than 1.6 times the capillary height, groundwater no longer directly involves in soil evaporation, but indirectly affects the water conversion in the unsaturated zone. Therefore, during the simulation period, the cumulative bare soil evaporation of the shallow groundwater depth was about 4 times that of the deep groundwater depth.