Groundwater recharge is critical to water circulation in arid and semi-arid regions. The accurate determination of groundwater recharge is required for assessing water resources and effectively managing groundwater, especially in water-limited areas. Based on field experiments and numerical models in a semi-arid region, this study assessed the effect of non-isothermal flow on groundwater recharge. A lysimeter was used in the Mu Us Desert, northwestern China, to monitor groundwater recharge from 1 June to 30 September 2018. The numerical models (isothermal and non-isothermal models) were calibrated with the measured soil moisture and soil temperature. Groundwater recharge was found to take up nearly 29% of rainfall. The non-isothermal model was capable of accurately assessing groundwater recharge based on the accurate calculation of evaporation. The isothermal model, however, underestimated the groundwater recharge by 13.2% and overestimated the evaporation by 16.2%. The isothermal model overestimated evaporation during the drying process. In contrast, cumulative net recharge was underestimated after heavy rainfall events. It was therefore suggested that the non-isothermal flux should be considered in semi-arid regions, especially when assessing groundwater recharge.