Precipitation is a driver of changes in the spatiotemporal distribution of phytoplankton communities. The ecological consequence of precipitation is important, but the underlying processes are not clear. Here we conducted an immediate prior- and after-event short-interval investigation in the Three Gorges Reservoir region, to test whether the short-term changes in the phytoplankton communities and functional groups could be predicted based on the precipitation level. We found that precipitation of moderate and high levels immediately changed the phytoplankton distribution and altered functional groups. According to structural equation model, the vertical velocity (lambda = -0.81), light availability (Zeu/Zmix, lambda = 0.47) and relative water column stability (RWCS, lambda = 0.38) were important parameters for phytoplankton distribution during the precipitation event. Water quality did not directly affect phytoplankton distribution (lambda = -0.11) and effects of precipitation on the water quality only lasted 1-2 days. The phytoplankton community was redistributed with some tolerance functional groups appearance, such as groups F, Lo, M and groups M, MP, TB, W1 appeared duringand after- precipitation event, respectively. We also found that mixing rather than flushing was the driving force for the decrease of phytoplankton biomass. Our study provided valuable data for reservoir regulation and evidence for predictions of phytoplankton during the precipitation events under different climate change scenarios.