Anticyclonic eddies (ACEs) shed from the Kuroshio intrusion are often in the path of internal waves (IWs) originated from the Luzon Strait to the northern South China Sea (NSCS). The knowledge of interactions between them have focused on physical processes, while little is known about their influence on the biogeochemical processes. Based on the two sets of high frequency time-series Lagrangian observations and model analyses in the NSCS, we show that the nutrients and phytoplankton in the euphotic waters were affected by IWs, but they could also be regulated by the ACEs. The phytoplankton biomass and community structure in surface water were mainly controlled by the properties of ACEs. Distinct vertical distributions of phytoplankton were attributable to the direct and indirect effects of combinations of these multi-scale physical processes. Multiscale process interactions would be important determinants of the structure and function of the marginal sea ecosystems.