Lake is an important water resources in Mongolia, which has undergone a large variation in past decades. However, it is still challenging to monitor long-term changes in lake water storage (LWS) due to the lack of lake level monitoring and long-term satellite altimetry data for Mongolian lakes. According to the Advanced Land Observing Satellite Digital Elevation Model (ALOS DEM) and the Joint Research Centre (JRC) dataset, we estimated the LWS changes of 55 Mongolian lakes (> 10 km2) from 1991 to 2020. The results showed that the LWS increased by 40.24 km3 from 1991 to 1997, especially for northwestern Mongolia with 31.47 km3. However, the LWS decreased by 32.44 km3 from 1998 to 2010, and the lakes in the northwestern and southern decreased by 20.24 km3 (62%) and 7.38 km3 (23%), respectively, and then the LWS continued to decrease by 10.22 km3 from 2011 to 2020. The precipitation was the primary cause of lake change, which could explain 45.13% of LWS change based on Generalized Linear Model, followed by temperature (26.33%) and irrigated area (16.72%). Analyzing the changing characteristic and driving mechanisms of LWS can provide a scientific basis for local water resources management and planning.