Integrating ecosystem services (ESs) to delineate ecological functional zones (EFZs) is fundamental in terrestrial spatial planning and ecosystem management. However, existing studies have largely overlooked the refinement of EFZs at local scales, which hinders targeted and multi-scale ecosystem management. This study introduced a “two-step refinement zoning method” to address this gap, first using a self-organizing feature mapping method to delineate EFZs at a township scale, and then applying a hotspot overlay analysis to refine the resulting EFZs by designating them with different grades at the village scale. The proposed method was applied in Wuhan City, dividing it into five types of EFZs with different ES combinations and land use compositions. Furthermore, 5.23% of villages were identified as level I areas of EFZs, serving as advantageous areas of dominant ESs in the study area. On this basis, diversified management strategies and conservation priorities were proposed. This study provides a theoretical and methodological reference for terrestrial spatial planning and sustainable ecosystem management.