Abstract: This study aims to analyze the response of phytoplankton communities in the northern South China Sea to mesoscale warm eddies. In the summer of 2021, 19 large-scale stations were set up in the sea area to collect phytoplankton water samples, and a series of analyses were conducted on the abundance, diversity index, evenness index, etc. of phytoplankton in the northern South China Sea during summer. A total of 307 species of phytoplankton were identified, belonging to 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; In the center of the mesoscale warm eddy, the chlorophyll maximum layer is deeper than that in the edge region, and the nutrient concentration distribution shows similar characteristics; The physical processes of mesoscale eddy have a significant effect on phytoplankton community structure, and the abundance of phytoplankton in the central region of the warm eddy is lower than that in the marginal region. GAM analysis showed that in the central region of the warm eddy, the diatom cell abundance began to decrease with the increase of temperature, which was related to the lower silicate concentration in the central region, resulting in the diatom cell abundance in the central region being 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 dominant species of diatom such as Thalassionema nitzschioides and Nitzschia spp., and the dominant species of dinoflagellates such as Gyrodinium spp. and Scrippsiella spp. further showed that the abundance of diatom in the central region of the warm eddy was smaller than that in the marginal region, while the cell abundance of dinoflagellate in the central region of the warm eddy was greater than that in the marginal region. Through the analysis of community characteristic index of warm eddy region, it was found 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.