Phytoplankton productivity and community structure in the East China Sea (ECS) play an important role in marine ecology and carbon cycle, but both have been changing rapidly in response to recent oceanic and atmospheric circulation changes. However, the lack of long-term records of phytoplankton productivity and community structure variability in the region hinders our understanding of natural forcing mechanisms. Here, we use the phytoplankton biomarker (brassicasterol, dinosterol and alkenones) contents as well as the ratios between these biomarkers in three sediment cores from the ECS shelf to reconstruct the spatiotemporal variations of productivity and community of diatoms, dinoflagellates and coccolithophores during the Holocene, respectively. During 9–7 ka, the ECS shelf was characterized by low phytoplankton productivity with low coccolithophore contribution, caused by the oligotrophic condition mainly owing to the restricted Kuroshio Current (KC) intrusion under low sea-level conditions, thus the lack of nutrient input. Phytoplankton productivity generally increased during 7–4.6 ka, in response to the initial intrusion of the Yellow Sea Warm Current (YSWC, a branch of the KC), bringing nutrient from the subsurface KC to the upper layer of the ECS for phytoplankton growth. Phytoplankton productivity continuously increased during 4.6–1 ka, due to an enhanced circulation system (YSWC and Yellow Sea Coastal Current (YSCC)) driven by strong East Asia Winter Monsoon (EAWM). Significantly, high alkenone contents and coccolithophore contribution in the eastern core F11A was associated with its location closer to the warm and saline YSWC, which was suitable for coccolithophore growth. Beyond diagenetic processes which could partly account for higher biomarker contents near core tops, elevated phytoplankton productivity during the last 1 ka might be induced by more nutrient supply from the intensified circulation system driven by enhanced KC and anthropogenic activities. The latter also resulted in high dinoflagellate proportions in all three cores. These temporal and spatial changes of phytoplankton productivity and community structure in the ECS during the Holocene corresponded to different mechanisms by the air-sea interaction, providing insights into distinguishing natural forcing and anthropogenic influences on marine ecology.