The Zhu III subbasin is one of three subbasins in the Pearl River Mouth Basin in the northern shelf of the South China Sea. The Zhu III belongs to a rift basin initiated in the Paleogene, being a part of the rifting lake group of Paleogene age in the Pearl River Mouth Basin. The evolution of the Zhu III subbasin can be divided into three stages: lacustrine facies of the early stage (Paleocene-middle Oligocene), bay facies of the middle stage (late Oligocene), and open shallow marine of the late stage (Neogene), forming, respectively, source, reservoir, and seal rocks. The lacustrine sediments include the Wenchang Formation (oil source rock) and the Enping Formation (gas source rock), which are the source rocks of two petroleum systems in the study area. The Zhu III subbasin experienced three obvious tectonic movements, of which the tenso-shear movement in the late Oligocene and extensional movement at the end of the middle Miocene formed the main oil-bearing structures in the study area. Oil and gas exploration results, synthetic study of geochemical and thermal modeling of the two source rocks, diagenesis and organic inclusions, and basin modeling show that there are two petroleum systems in the Zhu III subbasin: the Wenchang-Zhujiang(.) petroleum system in Wenchang B sag, and the Enping-Zhuhai(.) petroleum system in the Wenchang A sag. In the two petroleum systems, hydrocarbon generation, migration, and accumulation peaks are late Miocene-Holocene.