The assessment of ecosystem service (ES) supply and demand is crucial for the sustainable development of dryland drainage basins. The natural ecosystems in the Kaidu-Kongque River Basin have experienced severe ecological degradation in recent years, and the ES supply and demand were contradicted due to water scarcity and excessive water utilization. In this paper, the supply–demand of five key ecosystem services were evaluated, and their spatial matching was also analyzed to provide total insights. The services assessed were food supply, water yield, carbon sequestration, habitat quality, and windbreak and sand fixation. We utilized various models, including InVEST, RWEQ, and GeoDa, to quantify and analyze the spatial and temporal patterns of ecosystem service supply and demand between 1990 and 2020. Our findings indicate that the supply and demand for all ecosystem services in the basin have increased over the last 30 years. However, the spatial distribution of supply and demand for each ecosystem service is not completely consistent. Except for windbreak and sand fixation, where supply exceeds demand, there is a spatial mismatch between supply and demand for each service. Furthermore, we observed a positive and synergistic correlation between the supply and demand of each ecosystem service, with water yield services being the dominant and limiting factor. The spatial correlation between the supply and demand of ecosystem services was dominated by “low supply—low demand”, “high supply—high demand” spatial matching, and “low supply—high demand” mismatch, which could explain the variation in water yield from upstream to downstream. Based on our findings, we recommend policies and recommendations for ecological conservation and sustainable development in the Kaidu-Kongque River Basin. The ES supply and demand will become more reliable by increasing water supplies in the middle and lower reaches of the basin. Our results provide illumination for the maintenance and sustainability of ecosystem services in arid regions.