Phytoplankton is an important primary producer of water, and its functional group characteristics play an important role in maintaining the stability of aquatic ecosystems. In order to reveal the characteristics and construction mechanism of phytoplankton functional group community and its driving factors in river networks of megacity, 19 representative small and medium-sized rivers in Shanghai were selected to investigate the characteristics of phytoplankton functional groups and environmental factors at 40 sites. The results showed that a total of 175 species of phytoplankton in 8 phyla were identified, which could be divided into 23 functional groups, and B, D, J, MP, P, S1, X1, X2, X3 and Y were the dominant functional groups. The results of cluster analysis showed that 40 sampling sites could be divided into two characteristic groups： low nutrient （G1） and high nutrient （G2）. There were significant differences in Shannon-Wiener diversity index, Margalef index, phytoplankton functional group community structure and environmental factors between the two groups （P<0.05）. The modified stochasticity ratio （MST） and the decay relationship analysis showed that the community construction of phytoplankton functional groups in Shanghai River was affected by the environmental filtering and spatial diffusion limitation, and the stochastic process was dominant. The community construction of the low nutrient group （G1） was affected by environmental filtration, while the spatial diffusion affected the construction of phytoplankton functional groups in the higher nutrient group （G2）. Difference analysis and multiple regression analysis showed that total nitrogen, nitrite nitrogen, total phosphorus, conductivity and dissolved oxygen were the main environmental factors affecting the community structure of phytoplankton functional groups in Shanghai River. This study provides new information for in-depth understanding of the biodiversity and ecological function maintenance mechanism of river networks in megacities, as well as the protection of water ecosystems in urban river networks.