The South China Sea (SCS) is the largest marginal sea in the North Pacific with deep basins. The northern SCS basin is connected to the North Pacific through Luzon Strait and might be affected by the Kuroshio, while the southern basin is far away from the Luzon strait. To reveal the major difference and controls of the carbonate system parameters in the northern and southern SCS basins, a cruise was conducted to the SCS basin in June of 2017. Dissolved inorganic carbon (DIC), total alkalinity (TA), pH and dissolved oxygen (DO) were collected during the cruises.In the waters deeper than 2500 m, all the parameters were consistent between the northern and southern SCS basin. However, in the waters shallower than 300 m, the northern SCS was characterized by relatively lower temperature and pH, but higher salinity, DIC and TA, which might due mainly to the influence of the Kuroshio in the northern basin. In the Euphotic zone, the parameters in the northern basin showed significant diurnal variations, which was influenced mainly by the internal wave propagated from the Luzon Strait. However, the southern SCS was very “quiet” and the parameters were fluctuated within a very small range. Comparison and controlling mechanisms between the northern and southern SCS basins will be presented in detail.