The 15th Conference of the Parties (COP 15) to the Convention on Biological Diversity elevated biodiversity conservation to a global strategy, and China has been actively implementing the goals of the “Kunming-Montreal Framework”. Nevertheless, global waterbird populations are undergoing a marked decline, driven by the confluence of threats such as habitat loss, pollution, over-hunting, biological invasions, and climate change. This downturn is especially acute in Asia, making the protection of waterbirds and their habitats a central focus within the COP 15 framework. As the headwater region of six major rivers, including the Yangtze, Pearl, Red, Lancang, Nujiang and Irrawaddy, Yunnan possesses rich wetland ecosystem types and serves as a critical node in global waterbird migration systems. However, affected by climate change, agricultural expansion, and tourism development, wetland fragmentation in Yunnan has intensified, resulting in the continuous shrinkage of waterbird habitats. Although substantial resources have been invested in ecological restoration, challenges such as inadequate conservation resources and unclear priority sites persist. Therefore, identifying and conserving critical waterbird habitats in Yunnan Province has become a crucial aspect of waterbird conservation efforts. Based on field surveys conducted in 2017, 2021, 2022, and 2023, along with integrated waterbird data from the Global Biodiversity Information Facility (GBIF) and the website of the China Bird Report from 2014 to 2024, this study applied three internationally recognized criteria for identifying important waterbird habitats to determine the priority sites for waterbird conservation in Yunnan Province. On this basis, the Waterbird Habitat Importance Index was used to classify waterbird conservation priority sites into five levels of protection priority. Combined with the list of protected sites form the National Forest and Grassland Administration, the gaps in waterbird conservation were analyzed. The results indicated that: (1) A total of 10 waterbird species met the criteria for identifying priority conservation sites, including one Critically Endangered species, two Endangered species, three Vulnerable species, one Near Threatened species, and three Least Concern species. (2) A total of 41 priority sites for waterbird conservation were identified, classified into five protection priority levels (from highest to lowest): Category I (3 sites), Category II (3 sites), Category III (3 sites) Category IV (11 sites) and Category V (21sites). These sites were mainly distributed in western, northwestern, and central Yunnan. (3) Among them, 20 waterbird conservation priority sites were found to be in a protection gap, primarily concentrated in the western and central regions of Yunnan Province. It is recommended to enhance the protection of waterbirds and their habitats in these priority sites, incorporate unprotected gap sites into the wetland protected site system in the form of wetland parks or conservation zones, and strengthen long-term monitoring.