The Southern Indian Ocean is a major reservoir for rapid carbon exchange with the atmosphere, plays a key role in the world’s carbon cycle. To understand the importance of anthropogenic CO2 uptake in the Southern Indian Ocean, a variety of methods have been used to quantify the magnitude of the CO2 flux between air and sea. The basic approach is based on the bulk formula—the air-sea CO2 flux is commonly calculated by the difference in the CO2 partial pressure between the ocean and the atmosphere, the gas transfer velocity, the surface wind speed, and the CO2 solubility in seawater. However, relying solely on wind speed to measure the gas transfer velocity at the sea surface increases the uncertainty of CO2 flux estimation. Recent studies have shown that the generation and breaking of ocean waves also significantly affect the gas transfer process at the air-sea interface. In this study, we highlight the impact of windseas on the process of air-sea CO2 exchange and address its important role in CO2 uptake in the Southern Indian Ocean. We run the WAVEWATCH III model to simulate surface waves in this region over the period from January 1st 2002 to December 31st 2021. Then, we use the spectral partitioning method to isolate windseas and swells from total wave fields. Finally, we calculate the CO2 flux based on the new semiempirical equation for gas transfer velocity considering only windseas. We found that after considering windseas’ impact, the seasonal mean zonal flux (mmol/m2·d) increased approximately 10%-20% compared with that calculated solely on wind speed in all seasons. Evolution of air-sea net carbon flux (PgC) increased around 5.87%-32.12% in the latest 5 years with the most significant seasonal improvement appeared in summer. Long-term trend analysis also indicated that the CO2 absorption capacity of the whole Southern Indian Ocean gradually increased during the past 20 years. These findings extend the understanding of the roles of the Southern Indian Ocean in the global carbon cycle and are useful for making management policies associated with marine environmental protection and global climatic change mitigation.