In this study, we want to clarify the driving factors of phytoplankton community in a set of eutrophic lakes in the lowland areas of Huaihe River, one of seven biggest rivers in China. We analyzed the phytoplankton community of five lakes located in the lowland areas of Huaihe River using Reynolds functional groups (RFG) approach, with simultaneous measurement of several environmental variables in monthly sampling campaigns during 2 years. The annual average phytoplankton biovolume of the five lakes ranged from 3.7 to 9.9 mm3/L, with the highest values occurring during warm seasons. The shallow eutrophic lakes primarily contained mixing and low-light adaptive species with C and D groups as dominant all-round the year. Representatives of X2, Y, and W1 were predominant during the spring and the autumn with high nutrients and organic matter concentrations. Cyanobacteria were mainly represented by group S1 especially during the summer. Mixing, temperature, together weak light caused by phytoplankton biomass, could shape phytoplankton assemblage more than nutrients in the shallow eutrophic lakes with warm-temperate climate.