Marine sediments featuring special colors have always played an important role in disclosing regional or global environmental transitions and geological evolution. A deep well (Nanke-1), drilled on Meiji Atoll in 2017, penetrated Cenozoic reef strata in the central Nansha Block (also referred to as Dangerous Grounds) in the southern South China Sea (SCS) and revealed two pronounced variegated (containing colors of white, reddish and red brown) reef limestone layers in the Miocene. Similar large-scale variegated reef limestones have not been found in other reef drilling cores to date, so its coloration origin, formation mechanism and geological implications are unclear. Here, synthesized mineralogical, petrographic, and geochemical analyses demonstrated that the presence of trace amounts of amorphous microsized hematite with varying crystallinity imparted reddish or red brown colors to reef limestones. Hematite formed during meteoric water-induced karstification after the carbonate platform was exposed subaerially. Long-term exposures were mainly controlled by regional tectonic uplifts closely associated with the subduction of the proto-SCS, the seafloor spreading of the Southwest Sub-basin and the collision between blocks (i.e., the Sabah collision and the Palawan collision). The different tectonic settings have led to the different developments of carbonate platforms in the northern and southern SCS during most of the Early and Middle Miocene, but the major expansion of the high-latitude Antarctic ice sheets and the resultant significant drop in global sea level may have contributed to wide exposure of carbonate platforms both in the northern and southern SCS in the late Middle Miocene. Our studies demonstrated that the occurrences of variegated reef limestones in isolated oceanic reef carbonate platforms have great potential in indicating subaerial exposure, regional tectonic uplift or sea level fall.