Study regionThe Mainstream in the Tarim River Basin, Southern Xinjiang, China Study focusClimate change and human activities have significantly altered the water cycle, and water security evaluation and management are urgent. In arid and semi-arid areas, the assessment of blue and green water is particularly important. In this study, the MIKE SHE model is used to simulate the spatial and temporal changes of blue and green water resources in the mainstream of the Tarim River Basin (TRB) from 1990 to 2050 under land use and climate change conditions. The scarcity and vulnerability of blue-green water are introduced to evaluate the water security of the basin. The impacts of different land uses on blue-green water resources were also calculated according to the model zoning. New hydrological insights for the regionThe results indicate that from 1990 to 2050, blue water resources show a spatial pattern of gradual decrease from upstream to downstream. Compared to blue water, green water is dispersed more evenly over space. Future climatic scenarios will impact water security, as will changes in blue and green water security in terms of time and space. By comparing the influence of ecological water transport on the change of blue and green water before and after 2000, it was found that environmental water transport plays a certain role in improving the blue water scarcity in downstream of the TRB. The study is significant in maintaining regional water security and ecosystem stability.