Land use change exerts a significant effect on the Asian elephant's habitat, and understanding the impact mechanism is a prerequisite for effective protection for this endangered species. To explore the spatiotemporal processes and mechanisms of land use changes and their impacts on the Asian elephant's habitat, LandTrendr algorithm was used to detect annual natural forest disturbances in Nangun River Basin, a China-Myanmar cross border region, based on Landsat time-series images for 1988 to 2018 together with land use/land cover classification maps of 1988 and 2018. The Ecological Niche Factor Analysis (ENFA) model was employed to evaluate the habitat suitability of the Nangun River Basin for Asian elephants. The results show that (1) from 1988 to 2018, land use changes were mainly characterized by rubber plantation expansion and severe natural forest loss, and the areas of disturbed forest differed greatly between China and Myanmar. (2) Drastic deforestation resulted from remarkable rubber plantation expansion led to the area loss, and the decline of connectivity of the Asian elephant's habitat. (3) The Asian elephant's habitat in the basin was gradually encroached from the edge to the interior so that the upstream and downstream suitable habitats were isolated because of severe deforestation in the cross-border regions between China and Myanmar. Thus, reversing the expansion of tropical cash crops like rubber trees, to restore the habitat connectivity between China and Myanmar through establishing a cross-border basin-wide natural reserve is a critical path to protect Asian elephant and to mitigate human-elephant conflict.