According to the previous research, combining with the current hydro-geological investigation in the study area, this paper discusses the formation mechanisms of megadunes and lakes in Badain Jaran desert. It is found that lakes in the desert formed mainly as a result of the lateral recharge of groundwater both from Yabulai Mountain and megadunes. The formation of megadunes is closely related with the rainfall and groundwater in the area. The formation and coexistent relationship between megadunes and lakes are as follows: the megadunes formed firstly, and then the lakes appeared. That means megadunes are a necessary condition for the formation of lakes there.