There have been many studies conducted on the Eocene source rocks (Shahejie Formation Mbrs 1 and 3) (E2s1 and E2s3) of the Bozhong Sag, Bohai Bay Basin in East China. However, Oligocene source rocks (Dongying Formation Mbrs 2 and 3) (E3d2 and E3d3) have also made significant contributions to petroleum accumulations in this region. Their organic matter (OM) enrichment mechanisms, environmental and ecological variations, and laterally variable facies remain subjects of debate, particularly in the lower Dongying Formation Mbrs 2 (E3d2L). Thus, we investigated the geochemical properties, depositional environments, and OM origins of E3d2L and E3d3 source rocks from seven prospecting wells in southwestern Bozhong Sag. Our findings indicate that E3d2L source rocks are of poor-to-medium quality, whereas E3d3 source rocks are classified as good-to-excellent quality. Notable differences in the geochemical characteristics between E3d2L and E3d3 source rocks were observed. Hierarchical cluster analysis identified five genetic organic facies. The E3d2L source rocks comprises facies D2-Ⅰ, D2-Ⅱ, D2-Ⅲ, and D2–D3, whereas E3d3 contains facies D3 and D2–D3, with D2–D3 being common to both source rocks. Additionally, an integrated OM enrichment model was established to evaluate Oligocene source rocks. The five genetic organic facies exhibit distinctive differences and some similarities regarding redox conditions, water salinity, and OM origins. Their geochemical characteristics within the same intervals display pronounced lateral heterogeneity from deep source rocks deposits to more marginal water depths. The established model provides guidance for the prediction and exploration of effective Oligocene source rocks in the Bohai Sea and research on the Paleogene and Neogene petroleum systems. Moreover, the integration of biomarkers and hierarchical cluster analysis methods for organic facies analysis has significant implications for predicting of source-rock heterogeneity in other lacustrine rift basins.