Abstract: As a widespread mesoscale physical process/phenomenon in the oceans, eddies have an important impact on the transport of matter and energy, which in turn regulate regional hydrodynamic and biogeochemical processes and exhibit significant ecological effects. This study analyzed the characteristics of cyclonic and anticyclonic eddies in the northeastern South China Sea using temperature, salinity, nutrient, and Chlorophyll a (Chl a) data obtained during the summer in 2020, coupled with the sea level anomaly (SLA) and surface geostrophic current data, to investigate the impacts of cyclonic and anticyclonic eddies on the distributions of nutrient and Chl a, as well as the underlying controlling mechanisms. The results show that the eddy activities in the northeastern South China Sea are obvious, with a cyclonic eddy and an anticyclonic eddy in the southwest of Taiwan Island (near 118°E, 21°N) and the northeast of the Xisha Islands (near 115°E, 19°N), respectively. The distributions of SLA and surface geostrophic currents also demonstrate the occurrence of this pair of eddies. At the same time, a pair of cyclonic and anticyclonic eddies also occurs in the central part of the investigated area (near 116°30ʹE, 19°30ʹN). The temperature, salt and density layers in the area affected by the eddies have a clear tendency to rise (cyclonic eddies) or fall (anticyclonic eddies), and the changes in the distribution of dissolved oxygen (DO) and nutrient in typical sections further indicate the existence of the eddies. Cyclonic eddies can transport nutrient-rich waters from the lower layer upward, thus promoting primary production and increasing Chl a concentration within the euphotic zone. This process contributes to a significant upward shift in the subsurface Chl a maximum (SCM) layer. In contrast, anticyclonic eddies tended to transport oligotrophic water bodies in the upper layer downward, which is unfavorable for primary production within the eddy, resulting in lower Chl a level and a deepening of the SCM. The analysis also pointed out that there were some variations in the depth and concentration of the subsurface nitrite maximum under the influence of the eddies, and its position was generally consistent with the SCM, which tended to be elevated and shifted downward within the cyclonic and anticyclonic eddies, respectively, which could serve as an indicator of eddy occurrence to some extent. In addition, the Chl a concentration outside the Pearl River Estuary is relatively high as a result of the influence of shelf upwelling. This study provides a basis for further understanding of the biogeochemical-ecological responses to eddies in the northeastern part of the South China Sea.