Marine carbonates, including shallow-water carbonates and pelagic carbonates, precipitating from seawater and representing the largest sink of calcium (Ca) and carbon (C) at Earth’s surface, could record seawater chemistry. Therefore, marine carbonates help regulate atmospheric carbon dioxide (CO₂) concentration and eventually Earth’s long-term climate change. Calcium stable isotope geochemistry is a powerful tool to reconstruct paleo-seawater Ca isotopic compositions (δ^44/40Ca_sw) and to constrain the global Ca and C cycles over geological history. Here, we present a Neogene record of δ^44/40Ca from pure dolomites of the core XK-1 in the South China Sea. We propose that the dolomites formed in seawater-like fluid-buffered diagenetic environments near the seawater-sediment interface. We demonstrate that XK-1 dolomites display no Ca isotope fractionation from seawater, and hence may serve as good archives of contemporaneous seawater δ^44/40Ca. Further, we quantify respective contributions of shallow-water and pelagic carbonates in sequestering carbon over the Neogene, using a Ca isotope mass balance box model. We find that more CO₂ may have been sequestered by pelagic carbonate burial during global cooling. The enhanced continental weathering, global cooling, sea-level fall, seawater chemical changes, and pelagic carbonate burial are tightly linked.