Shallow lakes in the middle and lower Yangtze River floodplain are important habitats for wintering waterbirds. In recent years, with the impact of fisheries increasing in the lakes, the wetland has become seriously degraded, which has adversely affected the foraging ecology of the wintering waterbirds. To gain insight into the characteristics of inland wetland resource partitioning of the waterbird assemblages in the shallow lakes, we collected data on foraging behavior of 30 waterbird species by instantaneous scan sampling during fieldwork from December 2008 to March 2009. Study sites were in Shenjin Lake, Caizi Lake and Wuchang lake, which are along the Yangtze River in Anhui Province, China. Clustering analysis was used to classify the wintering waterbird assemblages into different guilds. Detrended correspondence analysis (DCA) was also used to analyze the resource partitioning characteristics of the waterbirds. The results showed that the wintering waterbirds could be divided into four groups: deep water foragers (G1), shallow water foragers (G2), peckers and diggers (G3), and pickers in the mudflat (G4). G2 was the largest group with a total of 13 bird species, and of these the dominant species were swan geese and bean geese. The second largest group was G3 with six species, and the dominant species were tundra swan and Eurasian spoonbill. G4 was composed of five bird species, and the dominant birds were dunlin, spotted redshank and common redshank. The smallest group was G1, with only six species. The foraging substrates of the guilds were mainly mud flats and littoral zones. The first main axis of the DCA analysis was associated with wintering waterbird feeding behavior and movement ability; the second axis was associated with waterbird feeding space and foraging mechanism. The results showed that the foraging strategies and foraging sites together explain the partitioning of resources. Foraging behavior, movement pattern and foraging substrate were associated: the wintering waterbirds used different foraging strategies. Marsh birds mainly stayed feeding and pecking, mudflats birds used pause-travel foraging, and deep water birds mainly dived to forage. Thus, feeding behavior and food resources together with foraging strategy determined the characteristics of resources partitioning of the wintering waterbirds in the shallow lakes. Waterbirds in the grasslands mainly foraged by pecking, those in the mudflats used pause-travel foraging while the deep water birds foraged by diving. The results of this study showed that the large number of wintering waterbirds mainly foraged in the lake beach and shallow waters zone, which provide wintering food resources for waterbirds throughout the wintering season. During the wintering period, the decrease in abundance of vegetation and zoobenthos in the shallow lakes of the middle and lower Yangtze River floodplain severely impacts the wintering ecology of migrating waterbirds. We believe that it is important to maintain food availability in the different lake zones during the winter to maintain high waterbird diversity. However, further investigation is required to determine the type of food resources required in the inland lakes along Yangtze River during different periods.