Phytoplankton growth and micro-zooplankton grazing are regulated by temperature, nutrients, and light in the ocean. Because of the different vertical distributions of light and nutrients, there is often a deep chlorophyll maximum (DCM) layer in the water column, which is widespread and almost a permanent ecological structure in the tropical oligotrophic ocean because of the stable stratification of the water column. Most parts of the South China Sea (SCS) are oligotrophic with strong underwater irradiance and low surface layer nutrients due to the stratification. The nutrient level is too low to support a phytoplankton bloom in the surface water, however, there are numerous reports of bloom events in the SCS after typhoonsevery year. It is commonly accepted that vertical mixing can weaken the nutricline and bring deep nutrient-rich waters to the euphotic zone, fueling phytoplankton blooms in the euphotic zone. However, few studies have compared the responses of phytoplankton and micro-zooplankton to the fluctuations of light intensity and pulses of nutrients simultaneously. In this study, an incubation experiment was conducted in the basin of the SCS during a cruise to compare the responses of surface and DCM phytoplankton to elevated irradiance and nutrients. Additionally, dilution experiments in different nutrient and irradiance conditions with surface and DCM water samples were conducted to explore micro-zooplankton grazing activity and their roles in the surface and DCM layers. We hypothesized that the DCM phytoplankton could be the seed population when the deep water is mixed upward with the surface layer in the case of a typhoon due to the changes in irradiance and micro-zooplankton grazing activity. The experimental results showed 1) micro-zooplankton grazing rates in the surface water were significantly higher than those in the DCM, and micro-zooplankton in the surface layer preferred the large size phytoplankton (>5 μm), whereas there was no such size selection in the DCM layer; UVR could promote the grazing rate of micro-zooplankton, whereas nutrient additions slightly decreased it; 2) the DCM phytoplankton assemblage responded more rapidly to the nutrient and light supplements and reached higher maximum biomass than surface phytoplankton, and the finial dominating size was larger in the DCM layer than that in the surface water. Therefore, the DCM phytoplankton assemblage is under less micro-zooplankton grazing intensity, and is more sensitive to light and nutrients. These results prove the hypothesis that DCM phytoplankton are seed populations when the deep water is mixed upward with the surface layer in a typhoon.