The Yellow River basin, which covers nine provinces and autonomous regions in China, is home to various types of wetlands. The wetlands in the Yellow River basin provide key breeding, wintering and stopover sites for migratory waterbirds along the East Asian-Australasian Flyway (EAAF). However, the Yellow River basin is also confronted with many ecological safety challenges, such as agricultural reclamation, urbanization and unequal distribution of water resources, which are posing a major threat to migratory waterbirds and their habitats. As a result, it is important to identify key habitats for waterbirds and assess their protection status. Compared with the Yangtze River basin and coastal wetlands, however, the Yellow River basin still lag behind in terms of survey and monitoring on waterbirds and their habitats, and no synchronized and systematic survey and monitoring activities have yet been conducted. For this reason, it is necessary to collect the survey data from different parties and to assess key distribution areas of waterbirds and their habitats in the Yellow River basin. According to the three internationally recognized criteria for identifying key habitats for waterbirds, we define the priority areas for waterbird conservation in the Yellow River basin, on the basis of collecting and collating waterbird survey data from domestic and international bird-watching websites (i.e., eBird, GBIF, and BirdReport), relevant literature and waterbird survey reports. The habitat importance index of waterbird is employed to rank the site priority of waterbird protection priority areas, and to categorize them into three priority levels: Classes I, II, and III. We have analyzed and identified the priority areas that have not yet been included as the protected areas for waterbirds based on the national list of natural protected areas. Our findings suggest that 47 priority areas for waterbird conservation have been defined in the Yellow River basin, which are mainly distributed in the middle and lower reaches of the river basin, particularly Henan and Shandong provinces. Fourteen waterbird species can meet the criteria of priority areas for waterbird conservation, among which two species are listed as critically endangered, one as endangered and five as vulnerable. Two, eight and 37 sites are listed as priority level of Classes I, II and III for waterbird protection respectively. 20 priority areas have not yet been included as protected areas for waterbirds, accounting for 42.55% of the total priority areas. These priority areas are mainly found in the middle and lower reaches of the Yellow River basin. Among three unprotected sites are identified as priority areas of Classes I or II respectively. We suggest that these priority areas should be incorporated into the wetland protected area system including nature reserves, protected areas or national parks, and long-term monitoring needs to be strengthened.