The coordinated development of the water–food–ecology (WFE) nexus is a practical issue that has to be addressed urgently for northwest China’s (WTL) sustainable development. Optimizing the linkage relationship and accomplishing the rational distribution of resources from the perspective of the supply and demand for ecosystem services (ESSD) are imperative. Thus, in this study, a numerical indicator system for ESSD from the perspective of the WFE nexus was constructed with the incorporation of the water and carbon footprint. Based on this premise, the ecological management zoning method was enhanced by integrating supply and demand risks, and optimization suggestions were proposed for various zones. The results showed that (1) carbon sequestration (CS), food production (FP), and water yield (WY) supply and demand significantly increased between 2000 and 2021. High ESSDs were concentrated in the west side of northwest China. Maize, wheat, cotton, vegetables, and garden fruits had a higher demand for ecosystem services (ESs). (2) The three ESSDs were bound in a synergistic relationship. The synergy between supply exhibited significant spatial heterogeneity, while the synergies between demand showed similar distribution patterns. (3) Regarding quantity matching, the supply for FP and CS surpassed demand, while the WY supply could not meet the demand. The three ESs’ supply and demand deficits rose. Ecological supply–demand ratio (ESDR) regional differentiation for the three ESs was apparent. Regarding spatial matching, FP and CS concentrated on low supply–low demand, while WY focused on high supply–high demand. FP risk was concentrated in Qaidam Basin, whereas WY risk was mostly in Hexi inland river basin (HX), the Yellow River Basin area (HH), and both sides of the “Qice line”. (4) The ecological management zones were formed by integrating WTL’s three dominant weak functional zones, four categorized strategy regions, and four governance models. This study can serve as a scientific benchmark for regional ecological management, which is significant in ensuring northwest China’s water, food, and ecological safety.