The unclear understanding of the source rock characteristics for the Paleogene Dongying Formation in the Bozhong Sag leads to the lack of cognition in oil and gas exploration. This research systematically evaluated the discrepancy in geochemical characteristics of source rock intervals in the Dongying Formation based on detailed analysis using Rock‐Eval pyrolysis, total organic carbon (TOC), vitrinite reflectance (Ro), maceral components, stable carbon isotopes and biomarker parameters. It discusses the organic matter sources, depositional environment, thermal maturity and hydrocarbon generation potential in the source rock intervals of the Dongying Formation. The organic matter abundance in the third member (E3d3) and lower sub‐member of the second member (E3d2L) of the Dongying Formation is higher, with an average TOC of 2.08% and 1.03%, respectively, indicating that these source rock intervals could have good and excellent quality. The source rocks of the Dongying Formation predominately contain exinite maceral group and type II1 and II2 kerogen. The thermal evolution is mainly in the low‐mature and mature stages. The organic matter sources in the Dongying Formation are mainly dominated by mixed origin (the carbon isotope reversal of aromatics also provides a potential explanation). However, the values of 1,2,5−/1,3,6‐trimethylnaphthalene, (1,2,5,6 + 1,2,3,5)‐tetramethylnaphthalene/tetramethylnaphthalenes, methyldibenzofuran/methylphenanthrene (MDBF/MP) and dibenzofuran/phenanthrene (DBF/PHEN) parameters in the E3d3 and some samples in E3d2L decipher relatively smaller values than other source rock intervals, proving the enhancement of the contribution of lower organisms. Moreover, the terrestrial input in the bottom‐up deposition process of the Dongying Formation gradually increases. The depositional environment reveals the Dongying Formation source rocks mainly developed freshwater sulphur‐poor lacustrine facies and shallow lake‐fluvial delta facies in an open clay‐rich sedimentary environment with poor water column stratification, belonging to the typical weak oxidation–reduction depositional conditions. The comprehensive geochemical evaluation concludes that the favourable supply of lower organisms and stable clay‐rich depositional environment in the E3d3 interval of the Dongying Formation are potential explanations for the formation of lacustrine source rocks with high organic matter abundance, intermediate thermal evolution and excellent hydrocarbon generation potential, providing a good foundation for the exploration and development prospects of hydrocarbons.