Lake Poyang is the largest freshwater lake in the Yangtze floodplain in China, with dramatic seasonal water level changes each year. The objective of the paper is to show the characteristics of phytoplankton functional groups and their relationship with environmental factors. Samples of water quality and phytoplankton were quarterly taken and analyzed at 15 sampling stations of Lake Poyang from 2009 to 2016. The phytoplankton function groups of phytoplankton were analyzed. The phytoplankton community structure and functional group characteristics of Lake Poyang were analyzed from 2009 to 2016. The results show that the phytoplankton in Lake Poyang can be divided into 27 functional groups, 15 of which (C, D, G, H1, J, Lo, M, MP, N, P, S1, Tc, Wo, W1 and Y) are dominant. Functional groups P, Y, MP, and D were dominant in 2009 to 2011. Functional groups P, Y, MP, H1, and Lo were dominant in 2012 to 2016. The successional routine of dominant phytoplankton functional groups in different phases are P, MP, Y, Lo, D in low water level phases, P, Y, D, MP, H1 in increasing water level phases, P, Y, D, MP, Lo, H1 in high water level phases and P, Y, MP, G in decreasing water level phases. RDA results showed that water level changes, water temperature, transparency, conductivity, suspended solids and nitrite are the most important environmental factors of phytoplankton functional groups in Lake Poyang.