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. In recent years, climate change and human activities have dramatically changed the hydrological conditions and natural habitats of lakes in the middle and lower Yangtze River floodplain, and the effects of these changes on waterbirds habitat have not been effectively evaluated. It is very important to understand the distribution dynamics of wetland waterbirds and analyze the distribution changes of simulated wetland waterbird habitats. Based on the MaxEnt model and the filtered citizen science data of herbivorous waterbirds in the middle and lower Yangtze River floodplain, this paper simulated the suitability and distribution trend of herbivorous waterbirds habitats of 25 lakes in the middle and lower the Yangtze River from 2012 to 2021, and explored the relationship between the change of inundation area of lake and the habitat suitability of herbivorous waterbirds. The results show that the spatial distribution of suitable habitats for herbivorous waterbirds in typical lakes in the middle and lower Yangtze River floodplain showed a decreasing trend from the surrounding area to the center of the lake. In the middle and lower reaches of the Yangtze River, the area of habitat suitability of herbivorous waterbirds greater than 0.5 was the smallest in 2013 (1580km²), and the area was the largest in 2012 (4018km²) except for 2014 (low fitting accuracy). The habitat suitability of Poyang Lake in the middle and lower Yangtze River floodplain has shown a downward trend in the past 10 years. The reason may be that the water level of Poyang Lake continues to decline and the water surface area decreases. Among the other lakes, Chang Lake and Wu Lake showed an upward trend, and the rest showed no significant upward or downward trend. The study also found that the inundation area was significantly correlated with the habitat suitability of lake herbivorous waterbirds. The inundation area of growing vegetation formed by water level difference provides habitats and food sources for herbivorous waterbirds, and the area of inundation area can be used as a predictor of habitat suitability of waterbirds. This study can provide a scientific method and result for the simulation and prediction of wetland waterbird habitat, wetland ecosystem management, and biodiversity protection.