After 2003, the river-lake relation between Poyang Lake and Yangtze River has been changed significantly in autumn. Mudflats were being exposed earlier than before 2003 and the area of wetland plants was increasing. The data from the multi-year survey around the lake from 1998 to 2020 show that the total population of wintering migratory birds is steadily increasing, but the population of geese is increasing sharply. In order to analyze the causes of migratory birds' habitat and population changes, we started from the coupling relationship of hydrology-mudflats-vegetation-geese. Based on the hydrodynamic model-the Environmental Fluid Dynamics Code(EFDC), the dynamic changes of waters and mudflats in the reserve before and after 2003 were analyzed in Duchang Nature Reserve, which had the most concentrated distribution of geese in Poyang Lake. According to the characteristics of cascade exposure of mudflat, habitat suitability index (HSI) was established based on the flooding duration and growth distribution of Carex spp and Polygonum criopolitanum. And the sensitivity of the habitat suitability model was analyzed in relation to the population changes of Anser cygruoles, Anser fabalis, and Anser albifrons. The results showed that after 2003, the mudflats in the same elevation zone were exposed about 30 days earlier during the receding period than before 2003, and the area of exposed mudflats on the same dates after 2003 was approximately doubled compared to the period before 2003. From 1990 to 2019, The HSI for geese showed an overall increasing trend. The exposure time of mudflats and their area shares in different elevation zones of 9-12 m were the main factors of interannual variation of HSI. The correlation analysis showed that the number of Anser cygruoles, Anser fabalis and Anser albifrons increased significantly with the increase of HSI, and showed an exponential curve. When the HSI was greater than 0.5, the number of geese increased sharply, especially in 2017-2019, and the main reason for this phenomenon was that the mudflat exposure process matched the migration rhythm of geese. Therefore, based on the results and discussion, the appropriate exposure time window of mudflat was determined-from September 15 (258th day of the year) to November 4 (308th day of the year). The suggestions for wintering geese habitat protection were proposed under the change of river-lake relation between Poyang Lake and Yangtze River. The findings of this study can provide scientific basis for the regulating scheme of eco-hydrological process based on the protection of wintering geese.