The Pearl River Mouth (PRM) Basin is one of four Cenozoic basins in the South China Sea, and the Wenchang A Sag is a secondary depression in the western part of the basin. Both the Wenchang and Enping formations contain good source rocks in the western PRM Basin; however, only the latter has been considered a likely source of the discovered oil and gas. New data from fluid inclusions and the analysis of oil–source rock correlations for the WC10-3 oil and gas pools indicate two stages of petroleum charging, the earlier originating from the Wenchang Formation and the later from the Enping Formation. Kinetics of petroleum generation and structural evolution modeling were employed to further investigate the mechanism of formation of the WC10-3 oil and gas pools. It was shown that the crucial condition for the formation of pools is the time of development of the structural trap. The Wenchang Formation source rocks generated oil from 25 to 14 Ma in the possible source area of the WC10-3 oil and gas pools in the Wenchang A Sag, so that only traps formed earlier than this period could capture oil sourced by the Wenchang Formation. The Enping Formation source rock experienced its oil window from 18 Ma to the present with the main stage of oil generation from 15 to 5 Ma. During this period structural traps in the sag continued to form until movements became weak, so that most pools in the Wenchang A Sag originated from the Enping Formation source rock. The likely dissipation of oil and gas from the earlier stage of charging should be taken into account in assessing the oil potential of the Wenchang A Sag.