Climate change and increasing human activities have induced lake expansion or shrinkage, posing a serious threat to the ecological security on the Inner Mongolian Plateau, China. However, the pattern of lake changes and how it responds to climate change and revegetation have rarely been reported. We investigated the pattern of lake-area changes in the Dalinor National Nature Reserve (DNR) using Landsat imagery during 1976-2015, and examined its relationship with changes in climate and vegetation factors. The total lake-area in the DNR has decreased by 11.6% from 1976 to 2015 with a rate of −0.55 km 2 year −1 . The largest Dalinor Lake reduced the most (by 32.7 km 2 ) with a rate of −0.79 km 2 year −1 . The air temperature has increased significantly since 1976, with a rate of 0.03 • C year −1 (p < 0.05), while the precipitation slightly decreased during 1976-2015, with a rate of −0.86 mm year −1 . The Normalized Difference Vegetation Index (NDVI) increased by 27.7% from 1976 to 2015, especially after 2001 when vegetation has been promoted greatly as a result of the successful ecological protection and restoration in the Dalinor basin. The decrease in lake-areas for the DNR exhibited a negative correlation with NDVI (r = −0.397, p < 0.05) during 1976-2015. It seems that decreasing precipitation drives the reduction in lake-area, while rising temperature and vegetation greenness accelerated this decreasing trend by increasing evapotranspiration. The continuous lake shrinkage increases the ecological risks to the habitat of birds, causing a challenge to the management in the DNR.