The tectonic evolution of the South China Sea is closely associated with multiple subduction-collision processes in Southeast Asia. When the collision of the Dangerous Grounds terrane with Sabah-Palawan Islands terminated is debated due to poor age constraints at the southern margin of South China Sea. A deep well drilled on Meiji Atoll penetrates Cenozoic carbonate strata in central Dangerous Grounds. Robust strontium isotope ages and laser ablation–inductively coupled plasma–mass spectrometry (LA-ICP-MS) U-Pb dates provide critical chronological constraints on the Cenozoic evolution of the southern South China Sea. A middle Miocene hiatus spanning 9 m.y. on Meiji Atoll is thought to be mainly caused by tectonic uplift in the central Dangerous Grounds. The uplift in the central Dangerous Grounds was accompanied by underthrusting beneath the southern Palawan margin and orogenic uplifting in north Borneo during the middle Miocene. Data interpretation indicates an active collision in the southern South China Sea during the middle Miocene. The regrowth of the Meiji Atoll above the middle Miocene hiatus represents the end of this collision event in the southern South China Sea at ca. 11 Ma, after the cessation of seafloor spreading, which occurred at ca. 15 Ma.