Abstract: The geochemistry of coral reefs provides evidence for surrounding seawater conditions and may reflect the paleoceanographic, paleoclimatic and paleoenvironmental variations at the time of deposition. However, coral reefs are apt to be altered by diagenesis during and after their formation, which can lead to substantial changes in mineralogy, geochemistry and biological characteristics. In such a circumstance, the geochemistry of coral reefs is not able to reflect the characteristics of the surrounding water. Therefore, the influences of diagenesis must be excluded before the geochemical indicators are applied to coral reef research if the surrounding water conditions are studied. Our study this time focuses on the cores from the well SSZK1 drilled at the Yongxing Island, Xisha Islands. Microfacies with different fossils and carbonate cements are studied in-situ based on mineralogy, petrography and geochemistry of the reef so as to explore the history of diagenesis. Observation of hand specimens and thin sections suggests that, the carbonate rock types from the well SSZK1 core are mainly composed of branching coral skeleton, bioclast and others fossils, such as calcareous algae, gastropod and foraminifera, dominated by aragonite, high-magnesium calcite and low-magnesium calcite. Early atmospheric diagenesis, which includes cementation, neomorphism and dissolution, play critical roles in determination of the composition of reef rocks. The in-situ analysis with electronic probe and LA-ICP-MS suggests that the diagenetic minerals in different diagenetic stages are extensively dominated by low-magnesium calcite. Diagenetic aragonite is only observed in some local fossils. The primary fossils are characterized by high Sr/Ca and Sr, with low Mg/Ca, while the diagenetic cements characterized by low Sr/Ca and Sr, with high Mg/Ca). It indicates that the coral reefs have been reformed by the diagenetic fluids of different origin, which controlled the mineralogy and geochemical characteristics of the coral reef in different stages.