Abstract: Two basins, the Wan'an and Mekong basins, occur in the southern part of the western continental margin of the South China Sea (SCS), separated by a swell called Con Son. The former contains natural gas, whereas the latter produces oil. In order to study the cause of the difference as such, heat flow background, structural pattern, sedimentary environment and hydrocarbon kerogen of the two basins are reexamined and compared in this work, based on existing geologic data and references. Research results indicate that in addition to the differences in contained hydrocarbon, there are differences in heat flow, structural pattern, sedimentary environment and hydrocarbon kerogen as well between the two basins. Affected by fault activities, the geothermal gradient and heat flow value of the Wan'an Basin are obviously higher than that of the Mekong Basin. In the Wan'an Basin, the major source rocks include the Oligocene to Early Miocene lacustrine-estuarine sediments deposited in a fault-depressed basin, and the kerogen of the Oligocene source rock mainly comes from lacustrine algae, aquatic plants and some higher plants, while the kerogen of Early Miocene mainly from terrestrial higher plants such as mangrove forest, dominated by type Ⅱ₂-Ⅲ of kerogen, which largely generates natural gas. In the Mekong Basin, however, the major source rock deposited in Oligocene is dominated by lacustrine sediment of rift type, with hydrocarbon generation material coming mostly from algae and aquatic plants, and the kerogen of type Ⅰ-Ⅱ that generates mainly oil. Therefore, it is concluded that the difference in structural pattern controls the sedimentary environment, the difference in sedimentary environment controls the hydrocarbon generation material, and the difference in hydrocarbon generation material controls the type of hydrocarbon generated.