Abstract: Lake Hongjian is the largest inland lake in the Mu Us desert. It performs functions of tourism, fishery and ecological wetland. In recent years, its comprehensive functions have been influenced with shrinking of its area. In order to make clear the lake area variation and its controlling factors, a time sequence of lake area variation since 2000 was constructed by using previous data and research results and inverting MODIS NDVI data to the lake area. The study shows that the lake area variation was controlled by precipitation before 1991. After 1991, the lake area decreased due to less groundwater recharge resulting from lowering of the water table caused by agricultural activities and less surface water recharge due to dam construction in the upstream rivers.