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Maintaining ecological balance relies on biodiversity, and habitat network construction plays an imperative role in preserving biodiversity in regional areas. Nevertheless, there is a problem with the current habitat network construction, which focuses exclusively on ecological benefits without taking other benefits into account as well. In this paper, six species of birds with varying habitat types and varying adaptabilities to city life are selected as target species to build a habitat network based on the InVEST model, Circuit Theory, and Linkage Mapper, focusing on nuclei, patches, corridors, and islands for the harmonious coexistence of human-green space-birds in the most densely populated area of Nanjing, and to refine landscape design techniques for habitat creation. Below is a summary of the main results. Firstly, there is a direct relationship between species distribution and migration capabilities and the urbanization adaptation capabilities of species. Meanwhile, habitat quality has a significant impact on bird species distribution. Furthermore, the habitat network in Nanjing’s main urban area has a distributed and partially degraded core area, a single connectivity structure with poor functionality, and significant fragmentation of habitat patches. Finally, as a result of the above results, two perspectives of ecological landscape planning and design are proposed to optimize the relevant green space landscape in Nanjing’s central urban areas based on biodiversity and satisfying the tripartite symbiosis of humans, green space, and birds in the city. By planning and implementing habitat networks, it is possible to enhance the habitat quality of urban green spaces to a certain extent and provide new ideas for the overall planning of urban–natural systems.