After the operation of the Yangtze-to-Huaihe Water Diversion Project, the water level rise will have certain submergence impact on the suitable wintering habitat for migratory birds (mudflats and herbaceous marshes), and adversely affect their habitat and food accessibility. Based on the interpretation results of remote sensing images corresponding to different water levels in Lake Caizi, this paper analyzes the effects of water level changes on the exposure of the mudflats and the herbaceous marshes in the Lake Caizi, and establishes the response function of the area of main wetland types to the water level changes. The results showed that there was a significant negative correlation between the habitat area of mudflats and herbaceous marshes and water level during the overwintering period. The area of mudflats and herbaceous marshes was 6057.6 ha and 4460.9 ha respectively at current water level of 6.97 m. When the water level rises to 7.5 m, it will lose about 13.7% of mudflats and 5.5% of herbaceous marsh habitats. When the water level rises to 8.1 m, it will lose about 16.8% of mudflats and 10.0% of herbaceous marsh habitats. When the water level rises to 8.6 m, it will lose about 30.4% of mudflats and 22.2% of herbaceous marsh habitats. From 1956 to 2015, the trend of water level and the probability of water level exceeding 8.1 m during the overwintering period of migratory birds both indicate that the engineering dispatching operation will have certain influence on the ecological hydrological process of the Lake Caizi. This paper on the one hand provides the basis for simulating the effects of different water levels on the area of main wetland types in Lake Caizi. On the other hand, it provides the scientific basis for the water level optimization of the Lake Caizi from the engineering perspective. However, due to the lack of data, this article has some limitations in fully explaining the relationship between the area of wetland types and habitat. It is suggested to implement experimental study on habitat adaptation and ecological environment monitoring during the overwintering period of migratory birds to further understand the response of suitable habitat, and important wintering bird population and distribution pattern to water level changes.