Coastal wetlands in mainland China are home to rich fishery resources, mangroves and seagrass beds. They are recognized as key part of global biodiversity, providing natural eco-safety barrier for the development of economically developed coastal regions in China. They are not only known as precious natural resources, but also key components of a biotic community of mountains, rivers, forests, cropland, lakes and grasslands for their important ecological functions and values. These wetlands provide important stopover sites for migratory waterbirds along the East Asian-Australasian Flyway (EAAF), supporting millions of migratory waterbirds of international importance along the EAAF. Since 1960, large areas of natural landscapes in mainland China's coastal zones have lost as a result of rapid economic development activities, such as over-exploitation of natural resources and land reclamation for construction and farmland. These activities have led to a dramatic decline in waterbird populations in the area, and the loss and degradation of natural wetlands have threatened the stability of species and population of waterbirds. For this reason, it is necessary to protect waterbirds species and their habitats. Identifying conservation priority sites, conservation priority levels and gaps for the migratory waterbirds are important preconditions for targeted habitat conservation. Integrated survey data were derived from birding websites, survey reports of waterbirds and published literature along the 11 provinces/municipalities in China. Then we used hot-spot analysis to identify conservation priority sites of the waterbirds. We also calculated the proportion of the species number of conservation gap sites to the maximum species number, and divided these proportions into three conservation priority levels (0.5 ≤ P_i ≤ 1, I; 0.25 ≤ P_i < 0.5, II; and 0 < P_i < 0.25, III). Based on the list of national natural protected areas, we defined the conservation gap of waterbirds. The results showed 65 conservation priority sites were identified along coastal wetlands in mainland China, and 76 species (including 18 threatened species) meeting the criterion of hot-spot analysis were recorded in these sites. The conservation priority levels of these sites belong to Levels I, II and III, which had 8 sites, 10 sites and 47 sites, respectively. The sites with conservation priority levels of I and II are mainly distributed in the north of Shanghai, while the sites with conservation priority Level III mainly occur in the south of Shanghai. 38 sites are yet to be put under protection, accounting for 58.46 percent of the total number of conservation priority sites, in which six sites belong to the conservation priority levels of I and II. To address this problem, we recommend that new protected areas should be established for the conservation gap sites with the conservation priority levels I and II, and be incorporated into the existing network of protected areas.