The Badain Jaran Desert was located at the northwest inland of China with drought and intensive evaporation. In stark contrast, there were dozens of permanent lakes inside the desert hinterland. Water recharge of the lakes in the Badain Jaran Desert has always been controversial. Based on water balance algorithm,this paper investigated the water recharging mechanism of the lakes. Dynamic observations of precipitation, evaporation, lake level and groundwater level were conducted in the Sumu Jaran lakes area. Based on the data analysis, a 3D model of groundwater was set up to reconstruct the seasonal dynamic characteristics of the groundwater level in the lakes area, and the water balance analysis was carried out. The results indicated that the precipitation wasn't sufficient to meet the water loss via evaporation, and leakage of deep confined water was important to maintain the lakes. Both the groundwater level and the lake level showed as a sine curve, and the changing range was 18 and 22 cm, respectively. The maximum and minimum value of groundwater level and lake level appeared in April and November, respectively. The average recharge rate of the Sumu Jaran lakes for many years was approximately 11620 m³/d, to which the rainfall and leakage of the deep confined water contributed 13% and 87%,respectively. The former was high in summer and low in winter, while the seasonal variation of the latter was not obvious. The deep confined water, ultimately, was probably formed with rainfall in the mountain areas around the southeast Badain Jaran Desert. No obvious water deficit needs to be covered by the groundwater that is transported to fractured zone from the remote area. The results can provide scientific gist for the rational use of groundwater in the Badain Jaran Desert.