From June 2008 to May 2009, the waterbirds were surveyed by line transects and point counts methods in Dongxi Lake, Wabu Lake, Longzi Lake, Tuo Lake and Nüshan Lake in Huaihe River basin, Anhui. A total of 61 species of waterbirds belonging to 7 orders and 13 families were recorded.Of them,32 species (52.46%) are winter visitors,14 (22.95%) summer visitors,2 (3.28%) residents and 13 (21.31%) migrant birds. 28 of the bird (45.90%) recorded are natatorial birds and 33 (54.10%) are wading birds. Among these water birds,3 are nationally protected as first-grade species in China,and 6 are second-grade species. The species richness of Shannon-Wiener index is highest in Tuo Lake (3.652); G index (3.16), F index (8.59) and the G-F index are also highest compared with other 4 lakes since 39 species or 63.93% of bird recorded in the survey were found here. From the up-stream to the down-stream of Huaihe River, the similar coefficient of waterfowl community in all the wetlands is varied between value 0.224 5-0.595 7. The similar coefficient of waterbird species is highest between Nüshan Lake and Tuo Lake. Tuo Lake is not froze in winter, therefore it thus plays an important role in waterfowl conservation due to it can provide stopover site and wintering area for the migration of waterfowl.