In order to identify sand moisture of the mega-dune area and water sources in the mega-dune formation in Badain Jaran Desert, a sampling study on 15 boreholes with a depth of 5 m belonging to a 1610 m mega-dune located in the east of Nuoetu with the largest height difference was conducted in May 2009. The results showed that, the depth of distribution of dry sand layer of mega-dune area in Badain Jaran Desert is deeper than that of the distribution of dry sand layer depth of the precipitation areas. Moisture of wet sand layer is lower than that of the area with more precipitation, which indicates that it is a normal phenomenon in the area that the moisture content of wet sand layer under the local climate conditions is less than 2%. Sand layer of water in Nuoetu mainly exists in the form of thin film of water. With the thin film of water down the process of infiltration, some gravity water appears changed by thin film of water. This shows that moisture in mega-dune area may be one of the sources of the lake and groundwater. Spatial differences of sand moisture in mega-dune area are significant. The high moisture is in low-lying land and flat, which is beneficial to the precipitation infiltration. Especially the existence of thin dry sand layers showed that the effect depth of evaporation on sand moisture was very small, and can effectively promote the atmospheric precipitation transforming into groundwater through infiltration, which is the reason for infiltration of precipitation to reach groundwater level and become the import source of lake water in extreme drought conditions. Moisture in the area has a positive balance of the display, which is caused by a quick sand moisture infiltration and the effect depth of evaporation was very small. This phenomenon belongs to the positive equilibrium of moisture which is decided by the attribute conditions of sand moisture.