Several recent studies suggesting that respiration and calcification activities by shellfish represent a net source of CO2. In order to the assess the effect of shellfish aquaculture on the sea-air CO2 flux, a Pacific oyster Crassostrea gigas aquaculture area which is located in East Gongjia Island, Rushan City, were selected as the investigation area. Based on the investigation data of pH, total alkalinity (TA), chla, etc. in October 2011, the concentration and horizontal distribution of dissolved inorganic carbon (DIC) system parameters were calculated. Moreover, sea-air CO2 fluxes and the contribution of phytoplankton to the sea-air CO2 flux were estimated. Results showed that the DIC concentration of surface sea water ranged between 1953.20 μmol/L to 2130.74 μmol/L, with an average of 2048.73 ± 57.19 μmol/L; the main component of DIC was HCO3-, which occupied 88.25%; the pCO2 ranged from 220.08 μatm to 262.29 μatm, with an average of 246.46 ± 23.00 μatm; the sea-air flux of CO2 ranged from -53.78 mmol/(m2.d) to -21.93 mmol/(m2.d), with an average of -42.09 mmol/(m2.d), which represented that this area acted as a strong sink of atmosphere CO2 in autumn; Carbon fixed strength of phytoplankton ranged between 460.27 to 725.64 mg/(m2.d), with an average of 593.27 ± 91.98 mg/(m2.d); the higher sea-air flux of CO2 was mostly contributed by the photosynthesis of phytoplankton; there was no significant difference between culture area and non-cultured area of sea-air flux of CO2, which indicated that the respiration and calcification activities of oyster had little effect on the CO2 flux.