Yancheng coastal wetland, as an important part of the East Asian–Australasian Flyway, provided habitat for more than 200 migratory waterbirds by rest and over-winter. After it was listed as a “World Heritage List” in 2019, the protection of waterfowl habitat in Yancheng coastal wetland has attracted extensive attention from the international community. As an indicator species of Yancheng coastal wetland ecosystem health, waterbirds have practical significance for the protection of Yancheng coastal wetlands. Due to the long-term impact of human activities, the waterbird habitats are facing the threat of habitat fragmentation and lose, posing a serious challenge to its survival and diversity. Based on the survey data obtained Gruiformes, Charadriiformes, and Anseriformes waterbirds during the whole years from 2017 to 2021, this paper used the Maxent software for modeling species niches and distributions, a comprehensive evaluation method based on fuzzy mathematics, and Linkage Mapper model to assess the habitat suitability distribution of waterbirds, identify protection gaps and potential biological corridors for waterbirds in Yancheng coastal wetland. The results showed that habitat suitability and anthropogenic disturbance were the decisive factors affecting habitat selection of waterbirds. The suitable habitats for Gruiformes, Charadriiformes, and Anseriformes waterbirds were 23868, 22670, and 24870 ha, respectively. The suitable habitat area of waterbirds was 121,930 ha, concentrated on the study area's central and southern coast. Sheyang estuary was identified as a vital conservation gap in the study area. Meanwhile, biological corridors of a total of 33 waterbirds were identified in the study area. The longest biological corridor was 18.78 km, and the shortest was 0.09 km. Our research can provide scientific support for Yancheng coastal wetland protection and the improvement of waterbird diversity, together with the achievements of an ecological and sustainable situation between environmental conservation and economic development.