The global decline of freshwater biodiversity caused by climate change and human activities are supposed to disrupt ecosystem services related to water quality and alter the structure and function of aquatic communities across space and time, yet the effects of the combination of these factors on plankton community ecosystem has received relatively little attention. This study aimed to explore the impacts of disturbances (e.g. human activity, temperature, precipitation, and water level) on phytoplankton community structure (i.e. community evenness and community composition) and function (i.e. resource use efficiency) in four subtropical reservoirs over 7 years from 2010 to 2016. Our results showed that community turnover (measured as community dissimilarity) was positively related to disturbance frequency, but no significant correlation was found between phytoplankton biodiversity (i.e. evenness) and disturbance frequency. Phytoplankton resource use efficiency (RUE = phytoplankton biomass/ total phosphorus) was increased with a higher frequency of disturbance with an exception of cyanobacteria. The RUE of Cyanobacteria and diatoms showed significantly negative correlations with their community evenness, while the RUE of Chlorophyta exhibited a positive correlation with their community turnover. We suggest that multiple environmental disturbances may play crucial roles in shaping the structure and functioning of plankton communities in subtropical reservoirs, and mechanism of this process can provide key information for freshwater uses, management and conservation.