The source rocks in the Zhu III sub-basin of the Pearl River Mouth Basin are mainly developed within the Eocene Wenchang Formation (E2w) and the Oligocene Enping Formation (E3e), which are widely distributed and have great resource potential. The source rocks in the Zhu III sub-basin are mainly type II1 kerogens to type II2 kerogens, with high organic matter abundance and in the mature stage. However, the source rocks in this area lack a systematic classification and interpretation, to distinguish the shore-shallow lake facies of the E2w and E3e, both having similar carbon isotope values and biomarkers. According to organic geochemical data from 67 specimens of source rocks and 45 data of biomarkers in the E2w and E3e of the Zhu III sub-basin, particularly the biomarker compound indicators, the following three tasks were performed: (1) The paleoenvironmental characteristics of the E2w and E3e were investigated. (2) The geochemical identification criteria were established, and the E2w and E3e source rocks were divided into five categories: the E3e river swamp facies, the E3e shore-shallow lake facies, the E2w fan-delta facies, the E2w shore-shallow lake facies, and the E2w profundal lake facies. (3) Biomarkers indexes for evaluating maturity of source rocks in Zhusan sub-basin are optimized and quantified. The results of this investigation effectively solve the problem of identification of the source rocks with similar geochemical characteristics in the western Pearl River Mouth Basin, laying a good foundation for oil source correlation and hydrocarbon exploration. Moreover, this research can provide reference for the division and evaluation of the source rocks in offshore lacustrine basins worldwide.