In recent years, the Nanpu Sag in the Bohai Bay Basin in eastern China has experienced great discoveries in exploration, and has become a sag most rich in oil and gas in the basin. However, the early evaluation believed that the source rocks were of low quality. Based on numerous samplings and analyses, this paper finds that Es-3(4) (the fourth sub-section of the third member of the Paleogene Shahejie Formation) is a high-quality hydrocarbon source rock, its TOC is above 5%. The thickness of high-quality hydrocarbon source rocks is 100 m and that of effective hydrocarbon source rocks about 250 m. The main buried depth of hydrocarbon source rocks is more than 3500 m, vitrinite reflectance (R-o) is more than 0.8%. The amorphous body and algae are an important source of organic matter in the hydrocarbon source rocks. The rocks are enriched with layers of clay and fine-grained calcite, which are the result of seasonal water stratification. The organic layer formed by algae breaking out and settlement is the main source of the organic-rich mudstone layer in Es-3(4) in the Nanpu Sag. The biomarkers in Es-3(4) reveal that the Es-3(4) oil shale has a higher content of 4-methyl steranes, which is significantly different from that in other source rocks. In addition, a detailed comparison of biomarkers and isotopes in the Es-3(4) oil shale and oil suggests that the oil in the Nanpu Sag comes mainly from the Es-3(4) source rock, which is an object of future exploration.