Poyang Lake, the largest freshwater lake of China, serves as a crucial wintering site for migratory birds in the East Asian–Australasian Flyway, where habitat quality is essential for maintaining diverse bird populations. Recently, the frequent alternation of extreme wet years, e.g., 2020, and dry years, e.g., 2022, have inflicted considerable perturbation on the local wetland ecology, severely impacting avian habitats. This study employed the spatiotemporal fusion method (ESTARFM) to obtain continuous imagery of Poyang Lake National Nature Reserve during the wintering seasons from 2020 to 2022. Habitat areas were identified based on wetland classification and water depth constraints. The results indicate that both extreme wet and dry conditions have exacerbated the fragmentation of migratory bird habitats. The shallow water habitats showed minor short-term fluctuations in response to water levels but were more significantly affected by long-term hydrological trends. These habitats exhibited considerable interannual variability across different hydrological years, affecting both their proportion within the overall habitat and their distribution within the study area. This study demonstrates the ability of ESTARFM to reveal the dynamic changes in migratory bird habitats and their responses to extreme hydrological conditions, highlighting the critical role of water depth in habitat analysis. The outcomes of this study improve the understanding of the impact of extreme water levels on migratory bird habitats, which may help expand knowledge about the protection of other floodplain wetlands around the world.