In order to determine incorporation of boron species, boron isotopic fractionation, and influence of trace elements on isotopic compositions of boron in corals (δ¹¹B_coral), concentrations of Mg, Sr, Na, B and δ¹¹B_coral in growing corals from the South China Sea were measured. Relative to seawater, Sr enriched while Mg depleted in corals in the South China Sea. Although the δ¹¹B_coral values were different from various species and were not closely correlated with the element concentrations in corals in the South China Sea, Mg(OH)₂ existed in corals can result in high δ¹¹B_coral. Thus, it is necessary to examine the existence of Mg(OH)₂and to choose the same species when δ¹¹B_coral is used in the δ¹¹B-pH proxy. Based on the measured δ¹¹B values of corals and coexisting seawater as well as the seawater pH in the South China Sea, a new isotopic fractionation factor a_4-3 between B(OH)4- and B(OH)₃ was determined to be 0.979. Besides B(OH)4- into corals, our results showed that B(OH)₃ may also be incorporated into corals with variable proportions. The incorporation of B(OH)₃ into corals may challenge the hypothesis of δ¹¹B_coral = δ¹¹B₄, resulting in increasing uncertainty to the calculated seawater pH values to the δ¹¹B-pH proxy. We suggested that a best-fit empirical equation between δ¹¹B of bio-carbonates and seawater pH needs to be established by the precipitation experiments of inorganic carbonates or culture experiments of corals or foraminifera.