Field observations demonstrate that calc-sinters occurred in the lakes of Badain Jaran Desert. 87Sr/86Sr ratios, 14C, δ13C and mineral compositions of calc-sinters, and 3He/4He, 4He/20Ne, δ18O,δD, pH and TDS of water from springs and lakes are analyzed in detail. The results indicate that the lake water is supplied through deep fault zone. The "kernel" of stabilized dunes in the Badain Jaran Desert perhaps consists of calc-sinters and calcareous cementation layers. Deep-seated groundwater effuses from this "kernel" and recharges to lakes in desert.Precipitation and snowmelt water from the Qinghai-Tibet Plateau is fed into the Badain Jaran Desert,Gurinai, Wentougaole and Ejinqi areas through the Xigaze-Langshan Fault zone. The isotopic compositions of groundwater in the Alax Plateau are abnormal due to the strong evaporation of the Gyaring and Ngoring lake water in the headstream of the Yellow River. Groundwater dissolves dissoluble fractions of rocks during its transportation through the fault zone and flows out of the mouth of spring in the Badan Jaran Desert. The dissoluble fractions are finally developed into calc-sinters and calcareous cementation layers around the spring. Calci-sinters are gradually largened and eventually emerge on the surface of lake water. Eolian sands accumulate on the surfaces of calc-sinters and calcareous cementation layers,and eventually develop into dunes. Invasion of magma causes an increase in the temperature of groundwater within the faults. Groundwater evaporation provides water vapor for the formation of humid stabilized dunes during its upwelling. Rhizoconcretions found in Yihejigede indicate that the dune was formed and remained immovable 4700 years ago.The height of the megadunes is proportional to thermal quantity carried by the groundwater.