Identifying dominant water stress on vegetation growth over the arid basins is essential to better understand ecosystems and water interactions, which are fundamental in managing regional water resources. The Kongqi River basin is an ecologically sensitive area with limited water resources in the northern part of Tarim Basin in northwest China. How is the spatial distribution of vegetation controlled by natural conditions and anthropogenic regulation of water resources is a concern for ecology system protection. This study explores the spatio–temporal variations in the remote‐sensing vegetation index across the basin and identifies water stress forces with the Mann–Kendall trend test and linear regression analysis. Results show that the controls of vegetation change are different among geomorphological units over the past 20 years. In the northern mountains, the increasing vegetation trend mainly responds to climate change, particularly to increased precipitation. In contrast, in the plain area, the vegetation change is controlled by changes in hydrologic and anthropogenic water stresses. A significant rise in surface water and groundwater utilization counteracts the negative effect of the increasing hydrologic water stress in the upstream oasis. However, the increasing anthropogenic water stress contributed to more than 50% of vegetation decay in the downstream area during 2004–2015. The ecological water conveyance beginning in 2016 has promoted vegetation restoration, but the effect decreased with distance to the upstream area and showed a delay in response. This study provides evidence for ecological consequence of anthropogenic water stress that is beneficial to improve water resources management and ecosystem restoration.