Mega-dunes in the lake group area of the Badain Jaran Sand Sea, China, are generally taller than dunes in the non-lake group area. This spatial distribution of dune heights may provide a new perspective on the controversy regarding the dunes’ formation mechanism. In this study, we calculated the relative heights and slopes of individual dunes based on a digital elevation model, and we confirmed the height distribution of abnormally tall dunes in the lake group area of the sand sea. It was also found that slopes of more than 10° in the lake group area are more common than those in the non-lake group area. Based on meteorological observations, coupled with the measurement of water content in the sand layers, we propose a conceptual model demonstrating that moisture exchange between the lakes and soil via non-rainfall water will humidify dune slopes and form a more favorable accumulation environment for aeolian sand, thus increasing dune heights. Although long-term observations are yet to be carried out, the present study can be used as evidence for understanding the basis of dune formation in the lake group area and assessing groundwater utilization in deserts.