The middle and lower reaches of the Yangtze River are key waterbird habitats along the East Asian ? Australasian Flyway. However, habitat degradation and fragmentation, driven by climate change and human activities, pose severe threats to waterbird diversity. This study utilized citizen science data and the MaxEnt model to predict potential habitats for 123 waterbird species, identifying biodiversity hotspots as ecological sources. By integrating circuit theory and ecological resistance surfaces, we delineated ecological corridors and “pinch points”. The key waterbird habitats, including ecological sources and pinch points, were overlaid with the existing protected areas to assess conservation gaps. Our results show that: (1) the total potential area for key waterbird habitats in the middle and lower Yangtze River is 30,322 km2, of which 27,669 km2 is ecological source area and 2,653 km2 is composed of pinch points; (2) although 26.85% of key habitats are protected, only 12.24% of ecological pinch points are, indicating a significant gap in the protection of highly connected habitats; (3) the total area of conservation gaps is 9,417.5 km2, with 44 habitats partially protected and 19 completely unprotected. Based on the spatial distribution of these gaps, we propose four key conservation strategies: establishing food resource corridors, optimizing multi-objective management of protected areas, restoring ecological connectivity in critical river sections, and prioritizing the inclusion of high-biodiversity areas in the protected area network. Incorporating flexible conservation approaches, such as Other Effective Area-based Conservation Measures (OECMs), can fill gaps in traditional systems and provide practical solutions for enhancing waterbird diversity conservation.