As a newly established World Natural Heritage Site, the protection of waterbird habitats in Yancheng coastal wetland has attracted extensive attention. In view of the importance of this area in global biodiversity and waterbird habitats protection, it would be of great demonstration significance to carry out network robustness research on waterbird habitats with spatial isolation characteristics to improve the quality of habitat protection of the heritage site. In particular, the research on biodiversity in the region has a high global impact, and the research on habitat network would increase important demonstration value for the research on habitat protection of other species of the same type of wetland in the world. Therefore, this study used the complex network theory, the ecological stepping stone principle, and the current model to analyze the current situation of the habitat network structure of the multiple waterbird guilds in Yancheng coastal wetlands and the network robustness under different scenarios. According to the results of scenario simulation, this study carried out optimization research on habitat network structure. The results showed that the important habitat areas of the three guilds were mainly distributed in the interior of each habitat and the area from Dafeng to Tiaozini, including 18 habitat areas in the north and 6 habitat areas in the south. The total area of the northern habitat area was equivalent to 1/2 of the southern habitat area, while the average area was only equivalent to 1/6 of the southern habitat area. From the view of the distribution of stepping stones, these stones mainly distributed near important habitat areas, and there were differences in different habitat sites. The average area of stepping stones in the northern habitat area was 84.17 hm², and the average area of stepping stones in the southern habitat area was 85.03 hm². The stepping stone network in the study area was composed of 35 important nodes and 153 general nodes, and there were differences in network structure elements from the north to south. Under the optimal protection scenario, the network robustness was good, and the nodes with large centrality value could support the connectivity of the whole network well. Finally, this study proposed a habitat network optimization pattern. After optimization, the average node centrality of stepping stones in the northern habitat area would have increased by 123.22, the number of stepping stones would have decreased to 78, the average node centrality of the southern habitat would have increased by 57.47, the number of stepping stones would have decreased to 47, and the spatial connectivity level of the habitat network would have increased.