Abstract: As a widespread physical process/phenomenon in the oceans, eddies play an important role in the transport of matter and energy, thereby regulating regional hydrodynamic and biogeochemical processes and exhibiting significant ecological effects. This study utilized data collected in the summer of 2020 from the northeastern South China Sea, including temperature, salinity, dissolved oxygen (DO), nutrients, Chlorophyll a (Chl a), sea level anomaly (SLA) and surface geostrophic currents, to analyze the characteristics of cyclonic and anticyclonic eddies in this region and explore their impacts and mechanisms on nutrient and Chl a distributions. The results show that the eddy activity in the northeastern South China Sea is highly dynamic. A cyclonic eddy and an anticyclonic eddy are identified in the southwest of Taiwan Island (near 118°E, 21°N) and the northeast of the Xisha Islands (near 115°E, 19°N), respectively, with their occurrences further corroborated by the distributions of SLA and surface geostrophic currents. A pair of cyclonic and anticyclonic eddies is also observed near the central survey area (near 116°30ʹE, 19°30ʹN). The thermocline, halocline, pycnocline, and subsurface high-salinity water within eddy-influenced zones exhibit distinct uplift (cyclonic eddies) or subsidence (anticyclonic eddies). Vertical distribution of dissolved oxygen (DO) and nutrient gradients on representative cross-sections further confirm the presence of these eddies. Additionally, eddies corresponded well with patchy high/low-value zones of hydrographic parameters, DO, and nutrients in horizontal distributions. Cyclonic eddies promote upward transport of nutrient-rich deep waters into the euphotic zone, enhancing primary production and increasing Chl a concentration, while also causing a marked shallowing of the subsurface Chl a maximum (SCM) layer. In contrast, anticyclonic eddies facilitate downward transport of oligotrophic surface water, reducing Chl a level and deepening the SCM layer. The study also reveals that there were some variations in the depth and magnitude of the subsurface nitrite maximum under eddy influence, aligning with the SCM trends (shallowing in cyclonic eddies and deepening in anticyclonic eddies), suggesting its potential utility as an indicator of eddy occurrence. In addition, high Chl a concentrations are observed outside the Pearl River Estuary, likely influenced by shelf upwelling. This research provides critical insights and data support for understanding the coupling mechanisms between physical, biogeochemical, and ecological processes in the eddy-dominated northeastern South China Sea.