Recently, increasing numbers of oil and gas reservoirs have been discovered in the Wenchang Depression, western Pearl River Mouth Basin, South China Sea, revealing prospects for hydrocarbon exploration. The Enping Formation (E3e) is a key target layer for the development of source rocks. However, previous work has only focused on lacustrine swamp source rocks of E3e in the Wenchang A Sag, without a systematic study of shallow lacustrine source rocks. In this study, the quality of E3e shallow lacustrine source rocks is reevaluated, and the hydrocarbon generation and expulsion characteristics are analyzed using relevant geological data and constructing a conceptual model. The results show that the E3e2 source rocks have greater thickness (50–600 m) and similar organic matter abundance (0.5–2.5%) compared with the E3e1 source rocks (50–500 m and 0.5–2.5%). On the whole, the E3e source rocks were deposited in the continental environment and are dominated by Type II and Type III kerogen. Meanwhile, the E3e source rocks of the Wenchang A Sag are in the stage of mature to over mature, while those of the Wenchang B Sag are in the stage of low mature. Vertically, the hydrocarbon generation potential of the E3e2 source rocks is greater than E3e1. Also, the cumulative hydrocarbon production of steep slope in the Wenchang A Sag is larger than that in the Wenchang B Sag. In addition, the corresponding vitrinite reflectances of hydrocarbon expulsion threshold and peak are 0.72 and 0.96%, respectively. Horizontally, four hydrocarbon generation and expulsion centers were mainly concentrated in different subsags of the Wenchang A and B Sags for E3e. The maximum values of hydrocarbon generation and expulsion intensity for E3e1 are 1500 × 104 t/km2 and 1000 × 104 t/km2, respectively, while those for E3e2 are 1800 × 104 t/km2 and 1200 × 104 t/km2, respectively, with the expulsion efficiency of 75%.