To investigate the impact of oyster aquaculture on the greenhouse gas (GHG) emission of nutrient-rich waters, a 56 day mesocosm experiment was conducted. Five treatments were established, which included the control with no fertilization and no oysters (C), oyster without fertilization (S), fertilization without oyster (F), fertilization with standard density oyster (FS) and fertilization with high density oyster (FSP). The fertilization was designed to supply nitrogen and phosphorus at concentrations of 1 mg·L^-1 and 0.25 mg·L^-1, respectively. Pacific oysters (Crassostrea gigas) were stocked at a density of 27.78 g·m^-3 (FS) and 55.56 g·m^-3 (FSP), respectively. Greenhouse gas (GHG) flux at the sediment-water interface, nutrient concentration in interstitial waters and sediment physicochemical properties of six batches of samples were measured. Compared to the control (C), both fertilization and oyster presence promoted the sedimentation of particulate organic matter and significantly increased GHG flux at the sediment-water interface. In the F group, the peak fluxes of CO₂, CH₄ and N₂O reached (1 320.84±93.01) μmol·m^-2·d^-1, (1.02±0.09) μmol·m^-2·d^-1 and (0.55±0.05) μmol·m^-2·d^-1, respectively. However, under fertilized conditions, oyster aquaculture significantly inhibited GHG release. Compared to the F group, the FS group showed reductions in peak CH₄ and N₂O fluxes by approximately 32% and 31%, respectively, with a corresponding decrease in CO₂ flux of about 50%. More pronounced reductions were observed in the FSP group where peak CH₄ and N₂O fluxes decreased by approximately 66% and 63%, respectively, and CO₂ flux declined by over 70%. Our findings demonstrated that oyster aquaculture can effectively mitigate GHG flux at the sediment-water interface by reducing organic matter input in eutrophic waters, and improve the sedimentary redox environment to some extent.