The bird habitats change with seasonal migration. Based on this, the dynamic zoning management of nature reserves with the protection of rare and endangered birds as the main goal can effectively improve land use efficiency and help to coordinate biodiversity conservation with other ecosystem service functions. The MaxEnt model was used to predict the habitat range of birds in the breeding season and wintertime in Shengjin Lake National Nature Reserve, Anhui Province, and the dynamic zoning scheme was obtained by using spatial superposition analysis method. The results showed that the habitat suitability of birds in breeding season was affected by environmental factors such as population density, land use type, distance from settlements and distance from roads in wet season. Birds in winter were affected by environmental factors such as distance from road, population density, distance from water body in dry season and land use type in dry season. The catchment unit was analyzed as the dynamic regionalization unit of Shengjin Lake National Nature Reserve by using the ArcGIS hydrologic analysis tool. According to the characteristics of bird habitat seasonal changes combined with the superposition analysis of the analysis results, Shengjin Lake National Nature Reserve in Anhui Province was eventually divided into core habitat reserve, breeding season habitat reserve, winter habitat reserve and general control area. The core habitat reserves should be strictly to protect throughout the year, the breeding season habitat reserves and the winter habitat reserves should be strictly to control during the corresponding bird habitat period, and the non-habitat period can be rationally used, while the general control areas can allow the reasonable behavior activities throughout the year. The seasonal dynamic zoning scheme focuses on solving the contradiction between ecological environmental protection and community development in Shengjin Lake National Nature Reserve of Anhui Province, facilitates the formulation and implementation of ecological conservation planning decisions in the future, and further enriched the theory and method system of dynamic functional zoning research in nature reserves with seasonal resident species as the main protection objects. It provides a reference for formulating ecological management strategies to improve the efficiency of space utilization in nature reserves. In conclusion, it is suggested that in the ecological environment protection and community development of Shengjin Lake National Nature Reserve, regional control should be implemented according to the seasonal dynamic zoning characteristics of the reserve, and corresponding measures for the ecological environment protection and development should be formulated.