Abstract: This paper aims to study the response of phytoplankton communities in the northern South China Sea to mesoscale warm eddies. Phytoplankton water samples were collected in the 19 stations during summer cruise in 2021, and a series of analyses were conducted on the phytoplankton abundance, diversity index, evenness index, etc. A total of 307 species of phytoplankton were identified in 3 phyla and 82 genera. The results show that dinoflagellates and diatoms are the main phytoplankton groups in this area, with 176 and 129 species respectively. The main dominant species are Thalassionema nitzschioides, Nitzschia spp., Gyrodinium spp. and Scrippsiella spp.. The depths of chlorophyll maximum in the eddy center are deeper than those in the edge region, and the nutrient concentrations show a similar distribution pattern. The abundance of phytoplankton in the central region is lower than that in the marginal region, suggesting a significant effect of the physical processes of mesoscale eddy on phytoplankton community structure. The Spearman correlation analysis showed that the diatom cell abundance began to decrease with the increase of temperature in the central region of the warm eddy, and the diatom abundance in the central region is lower than that in the marginal region. In contrast, dinoflagellates have a higher cell abundance in the central region than in the marginal region. The abundance of Thalassionema nitzschioides and Nitzschia spp. in the warm eddy center region is lower than that in the marginal region, whereas the abundance of Gyrodinium spp. and Scrippsiella spp. exhibits the opposite trend. The analysis of community characteristic index of warm eddy region suggested that species diversity decreased significantly from marginal region to central region, and species distribution tended to be uniform. This study provides basic data for future exploration of phytoplankton response to mesoscale eddy.