Under global climate change, the ecological vulnerability issue in Mongolia has become increasingly severe. However, the change process of the ecological environment and the dominant driving factors in different periods and sub-regions of Mongolia are not clear. In this paper, we propose a new ecological vulnerability index for Mongolia using MODIS data, combined with the Geographical Detector and the gravity center model, to reveal the spatiotemporal changes and driving mechanisms of ecological vulnerability in Mongolia from 2000 to 2022. The results show the following: (1) the newly proposed remote sensing ecological vulnerability index has high applicability in ecosystems mainly in Mongolia, with an accuracy rate of 89.39%; (2) Mongolia belongs to the category of moderate vulnerability, with an average ecological vulnerability index of 1.57, and the center of vulnerability is shifting toward the southwest direction; (3) Tmax is the leading driving factor of ecological vulnerability in Mongolia, especially at high altitudes and in arid regions, where it directly affects vegetation growth, desertification, and water availability. The dominant interactive factors have shifted from Tmax boolean AND Tmin to Tmin boolean AND PRE, with PRE being the leading factor in the eastern, central, and southern regions of Mongolia, Tmax being the leading factor in the western region, and Tmin being the leading factor in the northwestern region. This study provides an index system for constructing the ecological vulnerability system in Mongolia and offers scientific references for the regional protection of the ecological environment in Mongolia.