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Although the Late Cretaceous marine incursion events (MI) significantly boosted organic carbon (OC) accumulation in the Songliao Basin, their net effects and accumulation mechanisms have long been debated. By integrating high-resolution geological data, multi-proxy paleoenvironmental analysis, and a machine learning-based approach for TOC prediction in Member 1 of the Qingshankou Formation, we reveal that total OC sediment accumulation rates (OCSAR) during high-intensity MI (HMI) increased by 28.8% compared to low-intensity MI (LMI) intervals, with the areal OCSAR of the study area rising from 0.43 × 10−2 to 0.55 × 10−2 GtC/(Myr·km2). The OC accumulation models during HMI and LMI are established: driven by the interplay of seawater influxes, basin morphology, and terrigenous inputs, which collectively modulated the bacterial sulfate reduction, redox conditions, and nutrient availability in the water column, the growth rate of areal OCSAR exhibited pronounced spatial heterogeneity, defining four distinct zones (I–IV). The validation case from the Nenjiang Formation demonstrates the robustness of the models. These findings establish MI as a global amplifier of OC burial in mega-paleolake systems and redefine resource development frameworks for lacustrine shales within MI sequences.