Rapid urbanization results in changes in land use, biogeochemical cycles, climate, hydrosystems, and biodiversity. Policy-makers have formulated ecological protection measures to facilitate sustainable development. However, traditional conservation planning mainly focuses on protecting specific green spaces, with limited consideration of the connectivity among green spaces from a habitat network perspective. Using citizen science data and occupancy modelling, we predicted habitat suitability, built habitat networks and identified key habitat patches based on their contribution to the functional connectivity of the habitat network for three focal water, forest, and open-habitat bird species. Based on the habitat requirement, small waterbodies and intermediate forest and open-habitat cover facilitate preserving water, forest and open-habitat birds. In regards to the network analysis, we found that key habitat patches with a high conservation priority were generally characterized by a relatively large patch size and/or located at critical positions in the habitat network (at central positions in the habitat network, or near large patches). We suggest that key habitat patches in restricted built-up areas are converted to protected areas or are kept as cropland under future urban planning. We emphasize the usefulness of the focal species concept in urban biodiversity conservation. Our study offers conservation recommendations from a habitat network perspective for urban planners to safeguard urban biodiversity and ecosystem health.