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 the natural eco-safety barrier for the development of economically developed coastal regions in China. They not only offer preciously natural resources, but also are key components of a biotic community of mountains, rivers, forests, croplands, lakes and grasslands for their important ecological functions and values. Coastal wetlands in China provide important stopover sites, breeding areas and non-breeding areas for migratory waterbirds along the East Asian-Australasian Flyway (EAAF). Nevertheless, the problems of wetland loss and function degradation still exist and are widespread due to a wide range of factors, such as fast industrialization and urbanization, the increased pressure of wetlands and their biodiversity loss, lack of coordinated wetland management systems, over-lapping of different administrative functions, and conflict among different sectors' policies on wetland management. Loss in coastal wetlands due to land use change resulted in dramatic change in habitat category and area, and further reduced the stability of waterbird population. However, it is still unclear where and how land use change has had impact on the distribution of waterbird habitats. In this study, we regarded coastal wetlands along the Yellow and Bohai Seas that a hotspot of land use change occurred as study area. We selected eight endangered species, i.e., Spoon-billed Sandpiper, Great Knot, Far Eastern Curlew, Nordmann's Greenshank, Black-faced Spoonbill, Chinese Egret, Relict Gull, and Saunders's Gull as targeted species. We combined species distribution model MaxEnt and GIS to estimate habitat distribution and their spatio-temporal changes between 2000 and 2020, and to assess the trend of waterbird population changes. Then we identified priority areas for conservation, and provided recommendation on conservation and management. The results showed that the waterbird habitats were mainly distributed in Bohai Bay, Laizhou Bay, and the coastal areas along the Yancheng and Rudong-Dongtai between 2000 and 2020. During that period, the habitat area of all eight species declined, among which the habitat area of seven species has lost more than 50%, and these areas occurred in Bohai bay and the coasts along the Yancheng, Tiaozini, Dongtai County, Xiaoyangkou, and Rudong County. Coastal wetland loss was a direct factor behind the decrease of waterbird habitats. The populations of seven species tended to decline. We identified priority areas for conservation with a total area of 240.32 km², and the coast of Rudong County was defined as a conservation gap area. We recommended expanding the boundary range of Yancheng world heritage site to include the unprotected area. It is necessary to improve conservation and management and reduce continuous loss of waterbird habitats. It is also important to engage the general public in the protection of waterbird habitats and promote the protection of new natural protected areas.