A shift in reservoir stratification and mixing significantly affects the water column ecosystem, which in turn leads to changes in phytoplankton abundance and community structure. To explore the effects of stratification and mixing on the phytoplankton community structure of a diversion reservoir, a 1-year survey was divided into a stratification period in 2020, a mixing period in 2020, and a stratification period in 2021, and redundancy analysis (RDA), variance partitioning analysis (VPA) and Pearson correlation analysis were used to analyse the key drivers affecting the phytoplankton functional groups, using Xikeng Reservoir as a case study. During the study period, 8 phyla, 69 genera and 9 major functional groups were observed in this reservoir. The dominant functional groups varied significantly, being X1 in the stratified period in 2020; P and D in the mixing period in 2020; and D, X1, and M in the stratified period in 2021. The phytoplankton diversity index was greater in the mixing period than in the stratification period, in agreement with the results of the aquatic ecological status evaluation (Q index, higher in the mixing period than in the stratification period). However, phytoplankton diversity of Xikeng Reservoir was of limited value in assessing the degree of water pollution, so should be considered in combination with the Q index. Water temperature (WT), mixing depth (Zmix), nitrogen–phosphorus ratio (N/P), and total nitrogen (TN) were important drivers of phytoplankton functional group dynamics in different periods. The study provides a valuable reference for assessing the relationship between environmental factors and phytoplankton communities, as well as for the evaluation and conservation of aquatic ecosystems in southern China's water diversion reservoirs.