The middle and lower Yangtze River floodplain is a hot spot for global biodiversity conservation and an important wintering ground for the East Asia-Australia migration route. Climatic conditions and human activities have dramatically changed the hydrological regimes and physical habitats of the middle and lower Yangtze River floodplain. However, the effect of water regime changes on the habitat suitability of wintering waterbirds has not been effectively evaluated. Based on the MaxEnt model and the citizen science data of herbivorous waterbirds, this paper simulated the habitat suitability and change trend of herbivorous waterbirds in lakes of the middle and lower Yangtze River from 2012 to 2021, and explored the influence of inundation area of lake on the habitat suitability of herbivorous waterbirds. Among the 25 lakes in the middle and lower Yangtze River, the habitat suitability of Poyang Lake in the past 10 years showed a downward trend, Chang Lake and Wu Lake showed an upward trend, and other lakes did not show a significant upward or downward trend. There is a significant correlation between the inundation area of lake and the habitat suitability of herbivorous waterbirds, which can be used as a predictor of habitat suitability of waterbirds. The study provides scientific methods and result references for predicting the suitability of waterbirds habitats in lake wetlands and the impact of wetland changes on them.