Phytoplankton surveys were carried out in May and June 2022 around two different intensities of rainfall events to better understand how rainfall affect the phytoplankton community structure in subtropical reservoirs. In combination of taxonomic and functional group classification methods, the variability of phytoplankton communities before and after the two rainfall events were examined in this study using non-metric multidimensional scaling (NMDS), and the driving factors behind the structural succession of phytoplankton communities were investigated using redundancy analysis (RDA) and variance partitioning analysis (VPA). The results showed that 125 species of phytoplankton were detected in 8 phyla and 69 genera, and the functional groups were divided into 11 species, among which S1, SN, MP, and N were the main functional groups. The phytoplankton community structure changed before and after Rainfall I and Rainfall Ⅱ. The phytoplankton community evolved from Cyanobacteria to Bacillariophyta in Rainfall Ⅰ, and Bacillariophyta were dominant during the rainy period; whereas Cyanobacteria were always completely dominant in Rainfall Ⅱ, during which the phytoplankton community evolved slightly from Cyanobacteria to Bacillariophyta and Chlorophyta. In line with the succession of Cyanobacteria to Bacillariophyta or Chlorophyta, the relative abundance of functional groups SN and S1 decreased while that of MP or N increased during the rainy period. Redundancy analysis and Variance partitioning analysis showed that mixing depth (Zmix), water temperature, and nutrients jointly drove the succession of phytoplankton communities and the taxonomic group classification could better explain the changes of phytoplankton communities than the functional group classification. This paper can served as a reference for the investigation of phytoplankton response mechanisms in the presence of precipitation.