Seawater 87Sr/86Sr ratios have been used as a proxy for continental weathering flux and the partial pressure of atmospheric CO2 (pCO2) in Earth's past, but the fidelity of 87Sr/86Sr records in marine carbonates under diagenesis remains controversial. To investigate this issue, we undertook an integrated chemostratigraphic study of 87Sr/86Sr, δ13C, and δ18O in bulk carbonate from three cores of the South China Sea region: lithified bulk carbonate of Late Miocene to Holocene age in the 607-m-long Xike-1 core (0–11,942 kyr B.P.) from the Paracel (Chinese: Xisha) Islands, and unlithified carbonate sediment in two shallow (<5-m deep) pushcores from the Spratly (Chinese: Nansha) Islands, Jiuzhang A (0–680 yr B.P.) and Jiuzhang B (0–350 yr B.P.). The carbonate sediment of the Jiuzhang cores yielded 87Sr/86Sr signatures matching those of modern seawater, confirming that carbonate sediments can be faithful archives of contemporaneous oceanic Sr-isotopic compositions. Four diagenetic zones were identified in the Xike-1 core based on δ13C and δ18O patterns: meteoric (Unit I, 0–161 m), mixed-diagenetic (Unit II, 161–215 m), and marine diagenetic zones (Unit III, 215–577 m), along with a second meteoric zone (Unit IV, 577–607 m). The bulk‑carbonate 87Sr/86Sr profile was not strongly altered by dolomitization or other processes in any of the diagenetic zones (although minor effects were observed in the marine zone). This study concludes that marine carbonates are likely to retain primary seawater Sr isotopic signatures even after undergoing multiple stages of diagenesis. This study provides detailed 87Sr/86Sr secular variations and continental weathering history since 12 Ma.