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To estimate annual sea–air CO2 flux in the southern Yellow Sea (SYS), surface CO2 partial pressure (pCO2) was determined using high-resolution underway observations across four seasons. Surface CO2 exhibited large seasonal variation in the SYS, with high values in summer and low values in spring. Surface pCO2 had no clear relationship with sea surface temperature (SST) or sea surface salinity (SSS) on the seasonal timescale. Apart from the thermal effect, the main processes affecting surface pCO2 varied among seasons, i.e., photosynthetic carbon fixation from winter to spring, sea–air CO2 exchange from spring to summer, vertical mixing and sea–air CO2 exchange from summer to autumn, and vertical mixing and sea–air CO2 exchange from autumn to winter. In spring, sea–air CO2 flux ranged from − 77.3 to − 0.05 mmol m−2 day−1, with an average of − 18.9 ± 5.3 mmol m−2 day−1. In summer, sea–air CO2 flux ranged from 0.01 to 30.4 mmol m−2 day−1, with an average of 3.8 ± 1.6 mmol m−2 day−1. In autumn, sea–air CO2 flux ranged from − 16.1 to − 0.03 mmol m−2 day−1, with an average of − 2.9 ± 1.7 mmol m−2 day−1. In winter, sea–air CO2 flux ranged from − 36.7 to 10.9 mmol m−2 day−1, with an average of − 4.5 ± 2.2 mmol m−2 day−1. Annual sea–air CO2 flux in the SYS was calculated as − 5.6 ± 1.8 mmol m−2 day−1, suggesting that the SYS absorbs atmospheric CO2 at an annual rate of 2.1 ± 0.6 mol m−2 yr−1.