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Slowly sinking small particles in surface seawater are proven to be one of the major contributors to the mesopelagic carbon flux. Phytoplankton can respond rapidly to changes in the marine environment, so assessing the efficiency of their downward export can better constrain the relationship between carbon biomass and sinking fluxes. Here, we measured the sinking rates of individual phytoplankton (φindiv) after being subjected to Luzon cold eddy (LCE), warm eddy (WE) and spring warm pool (SWP), and explored the main influencing factors affecting cell sinking. The φindiv in the euphotic zone of the central South China Sea (ceSCS) was measured using the SETCOL method during the inter-monsoon period in April 2017. Diatoms (mainly rod-shaped) were sinking faster under the influence of SWP, with the highest carbon fluxes in the surface layer; WE leading to slow sinking of dinoflagellates, rapid sinking of cyanobacteria and a significant reduction in the number of phytoplankton species; diatoms sinking slowly due to the LCE. The φindiv of cylinder-shaped and rhombus-shaped cells in diatoms and fusiform-shaped and ellipsoid-shaped cells in dinoflagellates were significantly modulated by cell size. The setae structure of Chaetoceros can modulate the sinking behavior well in different environments. Our results indicate that in the open ocean, the shape and size of cells, the unique ecological niches of different species, and the original localization of cells are essential for the modulation of sinking. [ABSTRACT FROM AUTHOR]