Barium isotopes (δ138Ba) obtained in carbonates have a great potential for reconstructing past changes in marine productivity and associated biogeochemical cycling. Although coral skeletons and inorganic carbonates have been used as archives for seawater Ba isotopes, few studies have investigated other confounding factors that influence Ba isotope fractionation (e.g., vital effects and carbonate mineralogy), hindering their use as paleo-proxies. In this paper, we report Ba isotope data for multi-species corals, including paired sets of living and fossil coral skeletons in the inner shelf (Paipu Reef, Hainan Island) and the open-sea (Jiuzhang Reef corals) in the South China Sea (SCS). We also present Ba isotope datasets of bulk carbonate sediments from two shallow-water drill cores (A and B) in the Jiuzhang Reefs, SCS. The δ138Ba data for the Paipu Reef corals have a relatively narrow range of values (0.12‰ to 0.21‰, mean 0.17 ± 0.06‰; 2 SD, n = 8) regardless of living and fossil coral skeletons. The corals of Jiuzhang Reef show a relatively consistent δ138Ba value (0.30 ± 0.04‰; 2 SD, n = 4). The coral skeletal δ138Ba values show no significant differences across multiple species within the individual colony, which suggests that vital effects do not affect coral δ138Ba records. These findings, together with the fact that a relatively constant δ138Ba offset exists between coral skeletons and seawater, indicate that coral skeletons may be reliable archives for past seawater δ138Ba. All bulk carbonate sediment samples yield constant δ138Ba values of 0.38 ± 0.04‰ (2 SD, n = 30) with a fairly consistent deviation (Δ138Babulk_carb-sw = −0.21 ± 0.04‰) from the reported typical surface seawater of SCS. In addition, mass balance calculation suggests that Ba isotope fractionation between inorganic High-Mg calcite (HMC) and seawater is derived to be Δ138BaHMC-sw = −0.13 ± 0.12‰, exhibiting a difference less than Δ138Baaragonite-sw = −0.28 ± 0.04‰ in aragonite precipitation. Our findings suggest that shallow-water carbonates are reliable archives of past seawater δ138Ba when considering Ba isotope deviations during marine carbonate deposition.