Mesoscale eddies play an important role in regulating biogeochemical cycles. However, the response of biogeochemical variables to cold and warm eddies has not been well elucidated, mainly due to most previous studies relying on remote sensing techniques and lacking in situ observations below the surface water. Here, we used hydrographic and biochemical data from one survey in the northwestern Pacific to document the vertical biogeochemical structure of one cold and two warm eddies. We first compared the changes of key variables in the eddy core relative to eddy outside, explained the role of key layers (the mixing depth, pycnocline, nutricline, euphotic) in causing these changes, and then analyzed the main environmental factors affecting chlorophyll a (Chla) and phytoplankton communities. Finally we focused on the response mechanisms of key biogeochemical variables to the cold and warm eddies. The results showed that biological variables (Chla, microphytoplankton, picophytoplankton), salinity, dissolved inorganic nitrogen (DIN), dissolved inorganic phosphate (DIP), and dissolved inorganic silicate (DSi) in the cold eddy core increased by 0.2–134%, while in the warm eddy core, they decreased by 0.2–70% relative to the eddy outside. The cold and warm eddies were able to force the deep chlorophyll maximum (DCM), which rose or fell with the pycnocline, nutricline and euphotic depth (Zeu) as a whole. Cold eddies with a raised thermocline could lead to about 20 m elevated DCM and enhanced phytoplankton biomass when the nutricline and thermocline were coincident. In contrast, warm eddies drove isopycnals downward, resulting in a 10–25 m drop in DCM and a decrease in nutrient and Chla concentrations at the center of the eddies. The significant difference in the vertical structure of the phytoplankton community between the center and the outside of the eddy might be explained by the direct influence of both nutrient concentrations and stoichiometry changes. The contribution of microphytoplankton to total biomass was much smaller than that of picophytoplankton in oligotrophic waters where the DIN:DIP and DSi:DIN ratios are significantly low. Compared to nutrients, photosynthetically active radiation (PAR) might not be the main factor controlling phytoplankton biomass and abundance attributed to Zeu being consistently deeper than the mixed depth (Zm), whereas it was likely to be the key limiting factor affecting the vertical distribution of the phytoplankton community.