The stratigraphic evolution of low-latitude carbonate platforms, highly sensitive to sea-level changes, is often poorly constrained due to limited core data and discontinuous depositional records. This study elucidates the evolution of the Meiji Atoll, a representative low-latitude platform in the southern South China Sea (SCS), since the late Miocene, using the reef-penetrating core (Well NK1) from Nansha Island. By integrating facies analysis, sequence stratigraphy, and geochemical proxies, we identified two third-order sequences (SQ1 and SQ2), each comprising transgressive (TST) and highstand (HST) systems tracts. Geochemical data indicate that TSTs were associated with enhanced upwelling and nutrient availability, fostering algal productivity, while HSTs were marked by subaerial exposure. The overall retrogradational stacking pattern of the atoll reflects a dominant control by long-term sea-level rise, superimposed by eustatic fluctuations. Our findings confirm that eustatic sea-level variations were a primary factor controlling the stratigraphic architecture and development of Cenozoic low-latitude carbonate systems.