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Frequent storm surges often cause catastrophic impacts on human lives and the global economy; however, these phenomena are not well understood. In this study, a regional storm reconstruction is performed based on a grain size analysis and stratigraphic modelling of the accelerator mass spectrometry radiocarbon dates of benthic foraminifera from two neighbouring lagoon cores from Lingyang Reef in the Xisha Islands located in the northern South China Sea of the western Pacific. The dating results from the lagoon cores reveal a similar to 3500-year depositional history. Three different depositional units are recognized based on a time series of distinct grain-size variations that correspond to the following three stages of storm activity: intense and frequent storms from similar to 3500 to 3100 cal yr BP and 1800 cal yr BP to present and weak and infrequent storms from similar to 3100 to 1800 cal yr BP. A high sedimentation rate remarked by reverse and chaos age is observed from similar to 2800 to 2600 cal yr BP in both cores, and it was likely associated with a tsunami event. In addition, grain-size variability may be associated with changes over time caused by the synchronous Asian monsoon and may also be correlated with climate records retrieved from the ice cores from Greenland; thus, this variability could indicate pervasive global climatic teleconnections. The overall temporal patterns of the isolated coral branches and shells from the sediment sequences are well correlated with the high sea surface temperatures in the western tropical Pacific. We suggest that increasing sea surface temperatures in the future may lead to more intense storm activity in the western Pacific warm pool as the planet warms.