The Cenozoic carbonate rocks, which are distributed widely in the Pearl River Mouth Basin, were found to host the largest biogenic reef oil field on the sea in China and of important research value. Based on the Cenozoic tectonic evolution of the South China Sea and Cenozoic tectonic evolution of the Pearl River Mouth Basin, this paper presents the study of geological conditions of carbonate formation. The study found that the distribution of Cenozoic carbonate rocks in the South China Sea is closely related to the disappearance of the ancient South China Sea and the expansion of the New South China Sea, and the suitable window period for the development of carbonate rocks was the extension period of the New South China Sea, obviously controlled by the expansion of the New South China Sea. The two expansions of the New South China Sea in the Oligocene—Miocene were related to the Neo Tethys back arc spreading. The Pearl River Mouth basin developed two types of carbonate platform: the ancient uplift edge of carbonate platform and volcano uplift isolated carbonate platform. The distribution of ancient uplift or volcanic uplift, tectonic subsidence and the global sealevel fluctuation are the main controlling factors of carbonate rocks and reef development in the Pearl River Mouth Basin.