This paper describes the Quaternary evolution of Meiji Atoll (also known as Mischief Reef) in the southern South China Sea. Findings are based on a sedimentological and paleontological investigation of the uppermost 150 m of core NK-1. Through the Quaternary, open-lagoon sediments initially developed from ca. 2.6 to 1.6 Ma, which were succeeded by backreef sediments from 1.6 to 1.1 Ma, and subsequently by reef-flat sediments from 1.1 Ma to present, as the atoll evolved. The deepest depositional environments occurred between 2.0 and 1.6 Ma as a result of significant rates of subsidence in the Dangerous Grounds area. Coral abundance steadily increased during the Quaternary due to the secular eustatic sea-level drop and continuous high temperatures in the southern South China Sea. After the start of the Mid-Pleistocene Transition from 1.25 Ma, there was an increase in the amplification of short-eccentricity glacio-eustatic cycles, which resulted in two impacts. First, more frequent exposure horizons developed over the atoll due to an increase in amplitude of short-term sea-level fall events. Second, the occurrence of the thickest coral framestone units developed at around 0.8 Ma, perhaps linked to prominent short-term sea-level highstands (i.e., 125-ka cycle) and moderate subsidence rates. In summary, we document the Quaternary evolution of the Meiji Atoll, and show how variations in sea surface temperature, eustatic sea level, and tectonics have influenced its development. These findings have broader implications for understanding the Quaternary evolution of similar tropical carbonate atolls in the region.