The Kuroshio Extension(KE) System exhibits highly energetic mesoscale phenomena, but the impact of mesoscale eddies on marine ecosystems and biogeochemical cycling is not well understood. This study utilizes remote sensing and Argo floats to investigate how eddies modify surface and subsurface chlorophyll (Chl-a) concentrations. On average, cyclones (anticyclones) induce positive (negative) surface Chl-a anomalies, particularly in winter. This occurs because cyclones (anticyclones) lift (deepen) isopycnals and nitrate into (out of) the euphotic zone, stimulating (depressing) the growth of phytoplankton. Consequently, cyclones (anticyclones) result in greater (smaller) subsurface Chl-a maximum (SCM), depth-integrated Chl-a, and depth-integrated nitrate. The positive (negative) surface Chl-a anomalies induced by cyclones (anticyclones) are mainly located near (north of) the main axis of the KE. The second and third mode represent monopole Chl-a patterns within eddy centers corresponding to either positive or negative anomalies, depending on the sign of the principal component. Chl-a concentrations in cyclones (anticyclones) above the SCM layer are higher (lower) than the edge values, while those below are lower (higher), regardless of winter variations. The vertical distributions and displacements of Chl-a and SCM depth are associated with eddy pumping. In terms of frequency, negative (positive) Chl-a anomalies account for approximately 26% (18%) of the total cyclones (anticyclones) across all four seasons. The opposite phase suggests that nutrient supply resulting from stratification differences under convective mixing may contribute to negative (positive) Chl-a anomalies in cyclone (anticyclone) cores. Additionally, the opposite phase can also be attributed to eddy stirring, trapping high and low Chl-a, and/or eddy Ekman pumping. Based on OFES outputs, the seasonal variation of nitrate from winter to summer primarily depends on the effect of vertical mixing, indicating that convective mixing processes contribute to an increase (decrease) in nutrients during winter (summer) over the KE.