The calcium isotope composition of seawater (δ44/40Casw) records important information on the evolution of the calcium and carbon cycles over geologic time. Over the past two decades, many attempts have been made to reconstruct the Neogene δ44/40Casw variation using various calcium isotope records of seawater or seawater-like pore fluids. Nonetheless, large discrepancies still exist among these Neogene δ44/40Casw records. Here we report δ44/40Ca values in a suite of Neogene island dolomites (20.8–3.4 Ma, n = 18) from the South China Sea. Combining multiple geochemical proxies (δ44/40Ca, δ13C, and δ18O, this study; Sr/Ca, ∑REY, δ7Li, δ26Mg, 87Sr/86Sr, and Δ47, previous studies) and evidence from petrography, fluid inclusions, and magnetostratigraphy, we suggest that the dolomitization for these dolomites was buffered by seawater-like fluids in the shallow marine burial domain or even marine diagenetic domain (<180 m) over a considerable period of time (<2 Myr). Then, we apply the equilibrium calcium isotope fractionation factor between dolomite and seawater of −0.52 ± 0.20 ‰ (2SD, n = 13) estimated from the literature to these fluid-buffered dolomites and reconstruct a new Neogene δ44/40Casw record. After using the Locally Weighted Regression (LOWESS) curve fitting method, our dolomite-based δ44/40Casw record is consistent with the reconciled seawater record from other calcium isotope archives, including shark teeth, corals, foraminifera, brachiopods, barites, phosphates, and bulk pelagic carbonates. Our results support the use of fabric-retentive early marine diagenetic dolomites to trace the evolution of δ44/40Casw through Earth’s history.