Widespread and tremendously thick Cenozoic carbonate sequences are present along the margins of the South China Sea (SCS). However, most of the sequences have been drowned since the Late Miocene. The stratigraphic architecture of the carbonate platforms in the SCS can provide information on the tectonic evolution of the ocean basin. Based on 2D/3D seismic, well and regional geologic data, we have interpreted the Cenozoic SCS carbonate platforms along the continental margins. The carbonate platforms developed during rifting and initiated on the fault block of the conjugate rifted margins. Most of the carbonate platforms became drowned after the Middle Miocene. The Malampaya Carbonate Sequences, which have thicknesses of greater than 600 m, developed on a horst of an Oligocene rifted block. Tectonic subsidence provided accommodation for the growth of the carbonate platforms. Tectonic tilting, faulting, and the foreland bulge controlled the distributions, thicknesses, and horizontal seismic reflection variations of the drowned carbonate platforms. The tectonic evolution and relative sea-level fluctuations controlled the depositional cycles of the carbonate platforms. We quantitatively calculated the factors that affected the extension and subsidence rates using balanced cross section and backstepping techniques. Our results have demonstrated that the carbonate platforms flourished during the Middle Miocene due to stable tectonic conditions and shrank during the Late Miocene due to rapid subsidence. The relative sea level exerted a second-order control on the evolutionary trend of the carbonate platforms and a third-order control on the evolutionary periods in each stage.