The western region of Mongolia is characterized by an arid climate and a fragile ecological environment. It is a sensitive zone in response to global climate change and one of the major sources of dust globally. This region is home to numerous lakes, and their dynamic changes not only reflect global climate variations but also have implications for the global ecological environment quality. In this study, Landsat images were used as the data source, and Google Earth Engine (GEE) was employed to extract lakes with an area larger than 1 km2 from 1992 to 2021. The spatiotemporal characteristics of lake water area (LWA) changes were analyzed, and a structural equation model was applied to attribute the lake changes. The results indicate an overall trend of increasing lake area followed by a decrease in the study area. Specifically, lakes in the provinces of Khovd and Gobi-Altai exhibited a decreasing trend followed by an increasing trend, while lakes in the provinces of Uvs and Zavkhan showed an increasing trend followed by a decreasing trend. Three typical types of lakes, namely, alpine lakes, throughflow lakes, and terminal lakes, all exhibited a trend of increasing area followed by a decrease. The analysis of driving forces behind lake area changes reveals that climate change and human activities primarily exert indirect influences on the lake area changes in each province. Specifically, climate change and human activities lead to changes in soil moisture, which have a significant explanatory power for lake area changes. Regarding the typical types of lakes, climate change serves as the primary driving force for alpine lakes, while human activities are the main driving forces for throughflow lakes and terminal lakes.