As a newly established World Natural Heritage site, the conservation of rare waterbird habitats in the Yancheng coastal wetlands has attracted wide international attention. In view of the importance of this area in international biodiversity conservation and waterbird habitat conservation, the study of the current situation of rare waterbird habitat networks with spatial isolation features of great demonstration significance to improve the habitat conservation quality of the heritage site. Based on the data obtained from habitat suitability assessments of rare waterbirds, this paper used complex network theory, ecological stepping-stone theory and circuit models to analyze the current status and robustness of rare waterbird habitat networks in the Yancheng coastal wetlands. The results showed that the stepping stones of the red-crowned cranes and the Oriental storks were mainly distributed around important habitat areas, including aquaculture ponds and reed marshes, with areas of 1275.68 hm2 and 1247.74 hm2, respectively, while the stepping stones of Saunders's gulls were mainly distributed within the Tiaozini habitat site, with an area of 1180.76 hm2. The stability and connectivity of the habitat networks of red-crowned cranes and Oriental storks in the northern habitat area were better. At the Tiaozini habitat site, there was spatial isolation and low connectivity among the habitats and stepping stones of Saunders's gulls. In the optimal protection scenario, the stability and connectivity of the habitat network structure of red-crowned cranes and Oriental storks were the best, and the networks tended to exhibit assortativity. In the random destruction scenario, the connectivity of the habitat networks of Saunders's gulls was the lowest, and the network structure was the most fragile. Finally, the optimization and restoration patterns of habitat network based on improving the support capacity of important habitat nodes and the enhancement of the stability and connectivity of the stepping-stone networks were proposed.