Abstract: As an important indicator to evaluate the health of the urban natural system, urban biodiversity has received more and more attention from scholars and practitioners. From the perspectives of waterfowl habitats, waterfront habitat network and supporting ecosystem services of biodiversity, this research discusses a new approach for urban natural system comprehensive planning. It selects the Kunshan City, Jiangsu Province as the case of study, summarizes and identifies key indicators that influence the survival of waterfowls in built environment through literature review and on-site investigation, establishes a suitability analysis evaluation system of waterfowl habitats in Kunshan City, completes the existing waterfront habitat suitability mapping with ArcGIS, builds up a waterfront habitat network, and finally proposes strategies for building waterfowl habitats. It proposes three critical ideas for building up the waterfront habitat network for waterfowls, including 1) the identification of habitat sources and conservation of key habitat source areas; 2) the establishment of waterfront habitat corridors based on the suitable areas of high connectivity and high water coverage of lakes; 3) the addition of “stepping-stones” to functionally increase the connectivity of waterfowl habitats in the urban areas. This research aims to provide theoretical basis, evaluation standards and technical support for the conservation and increase of biodiversity in built environment, and build up a healthy relationship of people, water and birds based on the habitat network.