In order to study the relationship between structural composition of algae functional groups and environmental factors in the three typical shallow lakes of Changdang Lake, Ge Lake and Zhushan Bay, the water qualities of the three lakes are analyzed with Q index, Shannon-Wiener diversity index and TLI comprehensive eutrophication index based on the data of hydrology, water quality and phytoplankton from February 2019 to October 2020. Non-metric multidimensional scale(NMDS) is adopted to analyze the composition characteristics of phytoplankton community structure. RDA is adopted to analyze the relationship between phytoplankton functional groups and environmental factors. The results indicated that, the overall water qualities of Changdang Lake and Ge Lake are mild eutrophication, while the water quality of Zhushan Bay is moderate eutrophication except for that in winter. There are 96 species 61 genera 7 phyla, 129 species 75 genera 8 phyla and 124 species 53 genera 6 phyla of phytoplankton, which can be classified into 9,10 and 11 dominant function groups respectively, are identified in Changdang Lake, Ge Lake and Zhushan Bay, respectively. It is found that the common environmental factors of the changes in algae functional groups in the three lakes are water temperature, permanganate index and total phosphorus. The effect of total nitrogen and N/P ratio on the structural changes of functional groups in the three lakes are non-significant.