Many CO2-rich (up to 97% by volume) natural gas pools have been found in the continental margin basins of the northern South China Sea. By combining the geochemical data from 53 samples with their geologic backgrounds, this study investigated the origins and accumulation mechanism of CO2, and discussed the role of CO2 in driving oil as it charged the reservoirs. The results reveal that the CO2 gases in the Yinggehai basin originate mainly from the thermal decomposition of both Miocene calcareous shales and Paleozoic carbonates, and that CO2 from mantle degassing is only a minor contributor. The CO2 accumulations in the Yinggehai basin are mainly controlled by diapiric faults and episodic thermal fluid movements. The CO2 gases in the eastern Qiongdongnan and western Pearl River Mouth basins are mainly related to magmatic or mantle degassing, and the volatiles from magmatic degassing during the igneous intrusion stage are the most likely major source of CO2 in these reservoirs, with basement faults providing pathways for upward migration of CO2-rich mantle fluids. Natural displacements of oil by CO2 appear to be common in the eastern Qiongdongnan and western Pearl River Mouth basins. The CO2-flooded oil or gas reservoirs have two common features that the present CO2 gas pools or oil-bearing structures have residual oils representing prior charge, and are close to the basement faults that provide pathways along which the mantle-derived CO2-rich gas was migrated. The oils from prior hydrocarbon reservoirs have been naturally driven out by CO2 to form secondary oil reservoirs in the eastern Qiongdongnan and western Pearl River Mouth basins. Therefore, a full understanding of the origin and distribution of CO2 cannot just be used to trace hydrocarbon migration pathways, but also provide useful information for risk assessment prior to drilling.