Abstract: Based on thin-section observation, dating results, analysis of major and minor elements and carbon and oxygen stable isotopes, the sequence stratigraphy, sedimentary facies and geochemical characteristics of a 50.5-m drill core in the atoll lagoon were examined and its significance for paleoclimate and paleoenvironment was explored. Results show that sedimentary features well responded to the Late Quaternary sea level change and provenance. Using dating results, ten Pleistocene sequences were correlated with interglacial stages during Marine Isotope Stages 5-23. The gradual decrease in Sr and U values is due to the longer duration of exposure and meteoric diagenesis of the older sequence relative to the younger sequence in the carbonate platform, clearly indicating the existence of a sequence boundary. The reef facies were formed mainly during sea level fall, indicating progradational growth of the reef. Rapid sea level rise and slow sea level fall lead to reef facies preferring to grow in the highstand systems tracts of the sequences. Four potential sources were identified from the combined PMF (positive matrix factorization) factor profiles and factor contributions. Our results indicate the drilling reef layers in the modern lagoon can well reflect the sea level change controlled by the eccentricity cycles of 100 ka and that greater reef thickening of aggradational reef in the marginal platform than that of progradational reef in the lagoon, which enriched our understanding of the evolutional processes of the atoll with a deep lagoon.