Ecological zoning is utilized to identify critical ecological areas that are essential for preserving ecosystem integrity and stability. However, the zoning of fragile areas does not adequately address issues related to uneven distribution of ecological resources and the lack of synergistic management. To overcome this limitation, a comprehensive ecological zoning framework is proposed in this study, integrating the multidimensional Comprehensive Ecosystem Services Supply and Demand Ratio (CESDR) and Ecological Risk Index (ERI) within the Yellow River Basin (YRB), a prototypical ecologically fragile zone in China. Results indicate that: (1) the supply capacity of ecological resources in the YRB has gradually increased between 2000 and 2020, exhibiting a surplus in the south, a deficit in the north, and a spatial mismatch between the supply and demand of water resources; (2) the YRB is predominantly characterized by areas of medium to high ecological risk, which decreased by 83,640 km2 (10.34 %) between 2000 and 2020; (3) the YRB is classified into Ecological Resource Supply Zones (ERSZs), Ecological Resource Development Zones (ERDZs), Ecological Resource Redline Zones (ERRZs), and Ecological Resource Conservation Zones (ERCZs); (4) notably, the ERRZs, which predominate in the YRB, decreased by 20.88 % between 2000 and 2020, primarily transitioning into ERCZs (16.18 % increase) and ERSZs (3.49 % increase). It is proposed that ERSZs and ERCZs leverage ecological resource allocation to mitigate the imbalance between supply and demand within the YRB, enhance the ecological compensation mechanism for ERRZs to facilitate value accounting. This study provides insights into the sustainable development of fragile ecosystems.