Waterbirds serve as an indicator species, reflecting the condition of wetland ecosystems. Identifying the priority areas for protecting waterbirds diversity is immensely important for the functional zoning of nature reserves and wetland conservation and restoration. From May 2020 to April 2021, a continuous investigation and monitoring of the waterbird community in Hengshui Lake Nature Reserve was conducted. And the Geographic Information Science (GIS) software and structural equation model (SEM) were employed to analyze the structure and seasonal changes of waterbird community in different regions, the distribution pattern of waterbird diversity, and its driving factors. The results are as follows: (1) There were waterbird communities with geese and ducks as the dominant species in different areas of Hengshui Lake Nature Reserve. The highest species richness and Shannon diversity index of waterbird were observed in West Lake and Fudongpai river of Hengshui Lake Nature Reserve. The largest waterbird population was found in East Lake of Hengshui Lake, while Fuyangxin river had a relatively large population of curlew waterbirds. (2) Waterbird communities in different regions had obvious seasonal changes. The population of wading birds increased significantly in spring and summer, but only in East Lake, West Lake and Fuyangxin river of Hengshui Lake Nature Reserve became the dominant species of waterbird communities. After September, there was a notable increase in the number of species and population of swimming birds in each region, with geese and ducks gradually becoming the dominant population. (3) Areas with high species richness and population of waterbird were primarily located in the wetland restoration area, Fudongpai river, and areas on both sides of the small lake barrier in the nature reserve. The spatial distribution pattern of different groups of waterbirds were quite different, the distribution of geese and ducks was relatively dispersed, and the distribution of shorebirds such as waders and Gruidae and Ciconiidae were more concentrated. Habitat status was the main factor affecting the diversity of waterbirds in Hengshui Lake. (4) The conservation priority areas for waterbirds in Hengshui Lake Nature Reserve included the wetland restoration area and its surrounding areas, Nanlizhuang fishpond, Liangxinzhuang fishpond and its surrounding areas, Zimeidong island of East Lake, and areas on both sides of the small lake barrier, accounting for 8.94% of the total area of the nature reserve. The research results can provide a relevant basis for the functional zoning, formulation of protection strategies of waterbirds, and habitat conservation and restoration of Hengshui Lake Nature Reserve.