Variations in seawater-dissolved calcium ion (Ca2+) are small but substantial, which provides information essential to establish the oceanic calcium carbonate (CaCO3) dissolution flux. In this study, high-precision data of Ca2+ were collected in the South China Sea (SCS), the largest marginal sea of the western North Pacific, and its precursor, the West Philippine Sea (WPS), on the basis of two cruises conducted in 2007 and in 2008. An excess Ca2+ of 13 ± 5 μmol kg−1 was observed in the SCS subsurface water at 200–800 m relative to the WPS, and we suggest that such an excess is attributed to in situ CaCO3 dissolution at a rate of ∼0.5 mmol m−2 d−1 in the SCS shallow subsurface water. Through subsurface water outflow, this shallow-depth CaCO3 dissolution may provide a Ca2+ export flux of (0.8 ± 0.3) × 1012 mol yr−1 from the SCS to the WPS, establishing it as an important Ca2+ source from the SCS to the interior Pacific Ocean. This study indicates, for the first time, that along with the benthic processes, CaCO3 dissolution in waters at shallow depth in marginal seas could also contribute to Ca2+ and total alkalinity accumulations in the upper layer of the open ocean, which would ultimately enhance the buffer capacity of the world ocean in the context of rising anthropogenic CO2.