Growth and death are key processes to regulate the phytoplankton biomass and community structure, and further significantly affect marine ecosystem functions. However, in contrast to information about growth rates, there have been few reports of the regulation of death on phytoplankton community structure. In this study, we took the vertical stratified phytoplankton community in the oligotrophic ocean as the object, analyzed the difference in the proportion of dead cells among eukaryotic phytoplankton groups, focused on the effects of death on community structure variations and explored their mechanisms in response to environmental changes. The results showed that: 1) Cell size was the master trait of the community structure variations. Based on flow cytometry analysis, the eukaryotic phytoplankton were divided into five groups with successively larger cell size, i.e., Euk1, Euk2, Euk3, Cryp, and Euk4; 2) The group-specific proportion of dead cells increased with cell size, and the high proportion of dead cells in large-sized groups (Euk3, Cryp and Euk4) corresponded to low relative abundance. 3) On the vertical profile, the proportion of dead cells was also different among groups. The large-sized groups existed lowest proportion of dead cells and highest relative abundance in the deep chlorophyll maximum layer, but the small-sized groups (Euk1 and Euk2) existed no complete correspondence. 4) Above the nutrient replete layer, nutrient limitation-induced death existed in most groups, and the larger the cell size, the stronger the limitation. At the bottom of euphotic zone, all groups were restricted by light to induce death, but the differences among groups was not significant. These results indicated that the proportion of dead cells played an important role in the regulation of community structure, and groups of different size were regulated by environment to varying degrees, which further affected the community structure and function. This study highlights the differences in the regulatory community structure between phytoplankton mortality and growth.