Ecological management zoning is an important means to maintain regionally ecological security and achieve differentiated urban ecological governance. However, the existing zoning methods mainly focus on ecological functional attributes, with less consideration of the differences in linkage strength between ecological patches, and ignore the group structure of patches. In this paper, Wuhan City was taken as an example to construct an ecological network. From the perspective of ecosystem structure and function, combined with the spatial organization of patches and the strength of patch linkages, the cohesive subgroup method was applied to extract the ecological components that were closely connected, and the network was divided into heterogeneous groups, and regional coverage analysis was carried out based on the characteristics of network groups and the radiation range of ecological landscape, followed by a comprehensive evaluation of the zoning. The results showed that: (1) 86 ecological corridors connected 34 ecological patches in the study area, which further formed 8 ecological groups. (2) Most of these ecological groups had good internal connectivity, with strong connections between the northern groups and relatively weak connections between the southern groups. (3) According to the structure and function characteristics of the groups, they were divided into 6 network group zones. By comparing with the Wuhan economic development planning zones, the two zones had a high degree of consistency. (4) The network stability of the zone near the city periphery was good, while the stability of the central zone was poor. In addition, the 13 important patches and 16 important corridors within the zone were identified as key development and protection objects. (5) Based on the integrated characteristics of the zoning, six major zoning categories are established, namely as ecological shield area, ecological control area, ecological improvement area, ecological remediation area, ecological development area and ecological conservation area. In conjunction with these zoning categories, differentiated protection measures for ecological development in the zone were finally proposed. This research promotes an organic correlation between ecological function attributes and spatial structure attributes, culminating in the formulation of effective zoning strategies. In turn, this provides a new perspective for regional ecological management zoning and ecological protection planning.