Harmful algal blooms (HABs) have been investigated for their catastrophic effects on public health and aquaculture intensively, but the research about HABs effects on the diversity patterns and intrinsic functions of the plankton community based on a species identification with high resolution and accuracy has been scarce. We therefore investigated the shifts of plankton diversity via pyrosequencing during and around a natural dinoflagellate (Prorocentrum donghaiense) bloom and analyzed the effect of P. donghaiense abundance on the operationally-defined resource use efficiency (RUE) of plankton community to test our hypothesis that outbreaks of HABs will reduce RUE of the plankton community via shifting the plankton community structure, species composition in particular. We found that the species diversity of eukaryotic plankton community was significantly decreased during the bloom, as reflected in OTU (operational taxonomic unit) richness, and Pielou’s evenness index. Principal coordinates analysis indicated significant difference in plankton community structure between blooming and non-blooming periods. As hypothesized, the species richness was positively correlated to RUE (defined as the ratio of phytoplankton biomass to total phosphorus), and more importantly, the cell density of P. donghaiense exhibited significant negative correlation with RUE. Our results explicitlydemonstrated HABs reduce RUE via reducing species richness (corresponding to a less occupancy of the trophic niches), which supports the previously documented notion that niche partitioning enhances RUE (a key ecosystem function). Also, our work provides striking evidence for the relationship between plankton species richness (or diversity) and community function (resource use efficiency) via studying on HABs, a natural but exceptional phenomenon, in addition to revealing a profound consequence of HABs.