[Objective] The aim was to carry out study on characteristics of phytoplankton and its correlation with water environment in SFTWs. [Method] Based on the pilot-scale SFTWs in Hongqiao transportation hub of Shanghai,phytoplankton's community structure,diversity index and their correlation with water purification performance were investigated. [Result] 57 species of seven phylum of phytoplankton were detected in this tested river,including 12 species of Cyanophyta,2 of Cryptophyta,10 of Bacillariophyta,1 of Xanthophyta,7 of Euglenophyta,1 of Pyrrophyta and 24 of Chlorophyta,respectively. Additionally,it was found that Cyanophyta was the dominant phytoplankton,followed by Bacillariophyta and Cyanophyta. Biological density was far more than 10×105 ind./L,thus it could be considered that the river was eutrophic. The range of Shannon-Wiener index was 0.6-2.2,Pielou index was 0.5-2.5 and Margalef index's range was 0.35-0.85,which could further prove that the water was eutrophic. The biological density and species were significantly positively correlated with temperature and N content,indicating that the absorption of N by phytoplankton was the main N-removal pathway in SFTWs. [Conclusion] This study had provided basis for the river regulation and ecological restoration.