Nutrients associated with internal waves are known to perturb phytoplankton communities in oligotrophic oceans, but details of the relevant processes and mechanisms are unclear. Here we report insights about the impacts of internal waves on the phytoplankton community based on 154-hour time-series of observations in an oligotrophic basin of the South China Sea. We found that the temporal variations of phytoplankton communities in the upper, middle, and lower layers of the euphotic zone differ. We demonstrated that these changes probably resulted from the perturbation caused by internal waves. These results suggest that the structure of the phytoplankton community in oligotrophic oceans is best described by a three-layer system at steady state and that the perturbation caused by internal waves helps to reveal this structure. We believe that the paradigm of this three-layer structure will provide a new theoretical framework for the study of phytoplankton-based biogeochemical processes in oligotrophic oceans.