The coexistence of lakes and mega-dunes is a unique landscape of the Badain Jaran Sand Sea in China， and its formation mechanism has not been widely recognized. Some studies have found that the high content pore water may be important in the formation of mega-dunes， but more efforts are needed to research its recharge source. Based on the comparison of meteorological elements and the temporal and spatial distribution of shallow layer sand water content in three lake basins in the hinterland of the sand sea， combined with previous studies on water isotope and water movement， we found that the existence of lakes greatly increased the variation range of air relative humidity and shallow sand water content in the lake basin， and affected the distribution of water content with height. The correlation analysis shows that the main process controlling the change of water content of shallow sand layer is the water loss and replenishment caused by temperature fluctuation， while the water replenishment of shallow sand layer in the dry lake basin is mainly from advection water transport of wind. Although long-term quantitative observation of the water content of sand layers in different depth is still to be carried out， the existing evidence shows that the high soil water content of mega-dunes in the Badain Jaran Sand Sea is the result of local water vapor balance accompanied by the coexistence of lakes and mega-dunes. Water vapor from the lakes probably migrates into the sand layer gradually in the form of soil adsorption water or condensed water. This provides a new perspective for the research on the source of water in the sand layers， and also has a certain reference significance for the development and utilization of water resources in the hinterland of Badain Jaran Sand Sea.