Non-methane hydrocarbons (NMHCs) are important trace active gases that exert significant impacts on climate. Ubiquitous mesoscale eddies likely act as a key physical process regulating the marine emission of these gases, yet the underlying mechanisms remain poorly understood. Herein, we characterized the distributions and emissions of NMHCs in the South China Sea, with particular emphasis on the impacts of an anticyclonic eddy. Significantly lower NMHC concentrations were observed within the eddy-controlled region (201 ± 101 pmol L^−1) relative to the reference sites (433 ± 62.5 pmol L^−1). Downwelling in the anticyclonic eddy core reduced surface nutrient availability, suppressing the biological production and surface concentrations of alkanes and isoprene, whereas lower alkene levels were mainly driven by weakened photochemical production. NMHC sea-to-air fluxes dropped by 56 % within the eddy, which further diminished ozone and secondary organic aerosol generation by 59% and 60%, respectively. Overall, our findings elucidate the regulatory role of mesoscale eddies in NMHC dynamics, highlighting their critical function in shaping marine trace gas cycling and associated environmental consequences.