Understanding the history of the response of coral reefs to past climate changes can provide valuable information for predicting the future response of modern reefs. However, dating such ancient biotic carbonate is still challenging because of its sensitivity to diagenetic alteration processes, scarcity of well-preserved fossils, and low magnetic mineral content. There have been a long debates about the origin and evolutionary history of coral reefs in the northern South China Sea, mainly due to the lack of direct and reliable age constraints. This provides us with a good opportunity to verify the practicability of different dating approaches, especially the strontium (Sr) isotope analysis of bulk carbonate. Here, we retrieved a 972.55-m-long core from the Xisha Islands to provide a credible chronologic constraint on the carbonate platform evolution. The lithostratigraphy, strontium isotope stratigraphy, and magnetostratigraphy were analyzed throughout the whole reef sequence. The lithostratigraphic results show that the 873.55 m reef sequence developed on an ancient volcaniclastic basement and experienced multiple evolutionary phases. The 87Sr/86Sr results of all 100 bulk carbonate samples vary from 0.708506 to 0.709168 and show a monotonic increase with decreasing depth, except for a few outliers. Trace-element criteria and stable isotope (δ18O and δ13C) methods were applied to these bulk carbonate samples, and results imply that the primary or near-primary seawater 87Sr/86Sr values were likely preserved, although different degrees of diagenetic alteration occurred. In addition, the paleomagnetic results indicate 10 normal polarity and eight reversed polarity magnetozones. Based on the 87Sr/86Sr ratios of the selected 58 samples and paleomagnetic reconstruction of polarity reversals, the bottom of the reef sequence is dated to 19.6 Ma, and the observed polarity chronozones extend from chron C6 (19.722–18.748 Ma) at 866.60 m to present at the top. Based on the new data, we propose a new chronologic framework for the evolutionary history of the reef islands, where: (1) the reefs initiated in the early Miocene (19.6 Ma) and were drowned until 16.26 Ma; (2) during 16.26–10.66 Ma, lagoon to lagoon slope environments prevailed; (3) the lagoon environment progressively transformed into a reef crest environment from 10.66 to 4.36 Ma and 4.36 to 1.59 Ma; and (4) the reef started to be drowned again during 1.59–0 Ma. Our study provides a new and reliable chronologic constraint on the general evolutionary history of the reef islands in the northern South China Sea. Furthermore, the 87Sr/86Sr results from bulk carbonate indicate that strontium isotope stratigraphy is a powerful dating tool only when rigid sample selection, sequential leaching procedures, and strict trace-element and isotopic criteria are applied.