In order to study the correlations between the change of water quality and phytoplankton community structure during the process of Litopenaeus vannamei aquaculture, the water quality was tested and the changes of phytoplankton community structure were analyzed from April 2016 to September 2016 in an aquaculture farm in Fengxian District, Shanghai, and then the correlations between phytoplankton community structure and water quality factors were analyzed. The results showed that there were 7 phyla, 59 genera, 113 species (including 20 unnamed species), Chlorophyta > Bacillariophyta > Cyanophyta > Euglenophyta > Xanthophyta > Chrysophyta > Pyrrophyta, and 18 dominant species (including 3 unnamed species)——there were 10 dominant species (including 1 unnamed species) in the first season and 14 dominant species (including 2 unnamed species) in the second season. Dominant species were Bacillariophyta at beginning, then Chlorophyta and finally Cyanophyta. According to CCA analyzing, Chlorophyta is mainly affected by pH and nitrogen (including ammonia nitrogen, nitrate nitrogen, nitrite nitrogen), Cyanophyta by phosphorus (including total phosphorus and active phosphorus), and Bacillariophyta by temperature, so we should pay more attention to temperature, pH, nitrogen and phosphorus.