AbstractReasonable ecological function zoning is conducive to balancing ecological security and social development. Previous studies of evaluation for urban ecosystem services (ESs) have great progress. However, there is a lack of integrating ES stable hotspots into urban planning and refined management. In this research, we are interested in how hotspot identification can help promote ecological refined management. To achieve this, Chengdu-Chongqing urban agglomeration (CY) was chosen as a case study. First, we employed coefficient of variation and linear regression to analyze ESs temporal and spatial evolution trend from 2000 to 2017. Then, the stable ES hotspots were identified in the time dimension, and the results were superimposed on the dominant function zoning map obtained by a self-organizing feature map (SOFM). Finally, the refined zoning results were obtained, and we added corresponding control measures and policy guidance. The results showed the following: (1) from 2000 to 2017, water conservation (WR) and biodiversity conservation (Sbio) in the study area fluctuated greatly and showed a significant improvement trend on the whole; soil erosion protection (Spro), carbon sequestration and oxygen production (CSOP) showed a degradation trend in a few areas; (2) the area with at least one kind of ES stable hotspot accounted for 35.22% in the study area, and only 0.8% covered the four kinds of ES hotspots; and (3) the two-level zoning system of CY-refined management was designed. Eighteen cells have been designed within five main functional zones: urban agglomeration zone, modern agricultural development zone, ecological farming zone, ecological transition zone, and core ecological protection zone. Overall, the research based on natural ecological zoning management can provide a decision-making basis for urban planning, policy making, and sustainable development.