In this work, the seasonal variations of the carbonate system and air‐sea CO2 fluxes were investigated by two cruises in the southern Yellow Sea (SYS) and the East China Sea (ECS), which were significantly influenced by the Changjiang riverine inputs across seasons. Biological‐mediated change of dissolved inorganic carbon (DIC) was first quantitated through a three end‐member mixing model from winter to spring. Our modeling results suggested that DIC addition through biological remineralization persisted in the SYS during winter and spring, while DIC removal was evident in the Changjiang River Plume and the offshore ECS triggered by river inputs in spring. Horizontal and vertical mixing together constituted the largest contribution to the interseasonal variability of partial pressure of CO2 (pCO2) in the SYS (−69.5%), the river plume (−59.3%), and the ECS offshore (−43.8%), followed by temperature effects in the plume area (29.4%), and biological processes in the ECS offshore (24.1%) and the SYS (−7.7%), with air‐sea CO2 exchange contributing the least in both three subregions. The SYS, the river plume, and the ECS offshore all acted as atmospheric CO2 sinks in both winter and spring. Furthermore, their ability to absorb atmospheric CO2 increased from winter to spring, as reflected in a ∼1.8‐fold increase in the overall spring air‐sea CO2 flux compared to winter estimation.