Sustainable development and ecological environmental protection in arid regions are highly dependent on water resources. Exploring the quantity and supply-demand balance of blue and green water resources in arid river basins is essential for optimizing water resource management. We quantified the spatiotemporal distribution of blue and green water resources in the lower reaches of the Tarim River using a localized SWAT model, and assessed the water resource supply-demand balance in this region using the blue-green water scarcity index. The results showed that: (1) Both R² and Nash-Sutcliffe efficiency coefficient (NSE) in the calibration and validation period were greater than 0.7, indicating that the consistency between observed and simulated runoff met the research requirements. (2) The total amount of green water was generally higher than that of blue water. From 2000 to 2020, the proportion of green water exhibited an overall increasing trend, while the proportion of blue water relatively decreased, indicating an enhancement of the ecohydrological processes. (3) The supply-demand balance of blue and green water had generally improved, but with significant regional differences. The blue-green water scarcity index for each subbasin was less than 1, indicating that the available amount was generally higher than the demand, reflecting an alleviation of regional water resource pressure.