Abstract This study investigates the response characteristics of oceanic pCO2 in different regions of the Northern South China Sea (NSCS) to tropical cyclone genesis frequency (TCF) on interannual timescale, and clarifies the response mechanisms. Results show that reduced Sea Surface Temperature (SST) induced by TCs suppresses pCO2 in the northwestern SCS by increasing CO2 solubility. Stepwise regression analysis reveals that SST is the dominant impact factor, contributing 35.83% to pCO2. In the northeastern SCS, in addition to TC‐induced SST reduction, TC‐induced freshwater fluxes further reduce pCO2 by not only diluting surface CO2 concentration, but also suppressing vertical mixing and inhibiting the upwelling of dissolved inorganic carbon (DIC). SST, Sea Surface Salinity (SSS), and DIC are the dominant impact factors, contributing 24.41%, 30.94%, and 16.14% to pCO2. This study offers insights into TCF’s effect on the ocean carbon cycle in the NSCS on interannual timescale.