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Reef carbonates represent a practical option for continuous sampling in seawater 87Sr/86Sr values studies. A study of Sr isotopes is carried out for reef carbonates from the well “Xike‐1”, Shi Island, Xisha Islands, with the purpose of reconstructing the changing process of seawater 87Sr/86Sr values since the Neogene in the South China Sea (SCS). The results provide insights into the impact of paleoclimatic and paleoenvironmental factors on the seawater 87Sr/86Sr values in the SCS. Our study indicates that the 87Sr/86Sr values in reef carbonates have increased since the Neogene. Those variation process can be divided into three stages, which are the fluctuant rising stage (Early Miocene to Middle Miocene), the steady rising stage (Middle Miocene to Late Miocene), and the fluctuating stage (Pliocene to Quaternary), respectively. The change of terrigenous influx is the main factor controlling seawater 87Sr/86Sr values in the SCS. The 87Sr/86Sr values in reef carbonates are slightly higher than that in the coeval seawater, which reflects a semiclosed environment of the SCS relative to the open ocean. The variations of seawater 87Sr/86Sr values and terrigenous influx in the SCS have no obvious correspondence with the changes of seawater δ18O values recorded by the benthonic foraminiferal skeletons in the drilling core of ODP site 1148. Thus, paleoclimatic factor is unlikely to be the dominant factor for the changes of terrigenous influx in the study area. However, there is a good correspondence between the variation rates of the 87Sr/86Sr values, the accumulation rates of terrigenous materials, and the uplifting rates of the Qinghai‐Tibet Plateau. This indicates that the changes of terrigenous influx should be caused by enhancement of erosion, weathering, or transportation linked to the tectonic activities. The uplift of the Qinghai‐Tibet Plateau and the variations of uplifting rates should be the main factor controlling the variations of the terrigenous influx in the SCS, which would further influence the seawater 87Sr/86Sr values.

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