Deepwater oil and gas exploration has become a global hotspot in recent years and the study of the deep waters of marginal seas is an important frontier research area. The South China Sea (SCS) is a typical marginal sea that includes Paleo SCS and New SCS tectonic cycles. The latter includes continental marginal rifting, intercontinental oceanic expansion and oceanic shrinking, which controlled the evolution of basins, and the generation, migration and accumulation of hydrocarbons in the deepwater basins on the continental margin of the northern SCS. In the Paleogene, the basins rifted along the margin of the continent and were filled mainly with sediments in marine-continental transitional environments. In the Neogene–Quaternary, due to thermal subsidence, neritic-abyssal facies sediments from the passive continental margin of the SCS mainly filled the basins. The source rocks include mainly Oligocene coal-bearing deltaic and marine mudstones, which were heated by multiple events with high geothermal temperature and terrestrial heat flow, resulting in the generation of gas and oil. The faults, diapirs and sandstones controlled the migration of hydrocarbons that accumulated principally in a large canyon channel, a continental deepwater fan, and a shelf-margin delta.