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To reveal the causes of differences in the hydrocarbon accumulation in continental marginal basins in the central-southern South China Sea, we used gravity-magnetic, seismic, drilling, and outcrop data to investigate the tectonic histories of the basins and explore how these tectonic events controlled the hydrocarbon accumulation conditions in these basins. During the subduction of the Cenozoic proto-South China Sea and the expansion of the new South China Sea, the continental margin basins in the central-southern South China Sea could be classified as one of three types of epicontinental basins: southern extensional-foreland basins, western extensional-strike slip basins, and central extensional-drift basins. Because these basins have different tectonic and sedimentary histories, they also differ in their accumulated hydrocarbon resources. During the Cenozoic, the basin groups in the southern South China Sea generally progressed through three stages: faulting and subsidence from the late Eocene to the early Miocene, inversion and uplift in the middle Miocene, and subsidence since the late Miocene. Hydrocarbon source rocks with marine–continental transitional facies dominated by II–III kerogen largely developed in extremely thick Miocene sedimentary series with the filling characteristics being mainly deep-water deposits in the early stage and shallow water deposits in the late stage. With well-developed sandstone and carbonate reservoirs, this stratum has a strong hydrocarbon generation potential. During the Cenozoic, the basin groups in the western South China Sea also progressed through the three developmental stages discussed previously. Hydrocarbon source rocks with lacustrine facies, marine-continental transitional facies, and terrigenous marine facies dominated by II2–III kerogen largely developed in the relatively thick stratum with the filling characteristics being mainly lacustrine deposits in the early stage and marine deposits in the late stage. As a reservoir comprised of self-generated and self-stored sandstone, this unit also has a high hydrocarbon generation potential. Throughout those same three developmental stages, the basin groups in the central South China Sea generated hydrocarbon source rocks with terrigenous marine facies dominated by III kerogen that have developed in a stratum with medium thicknesses with the filling characteristics being mainly sandstone in the early stage and carbonate in the late stage. This reservoir, which is dominated by lower-generation and upper-storage carbonate rocks, also has a high hydrocarbon generation potential.