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Reconstruction of hydrocarbon generation history is essential to understanding the petroleum system. In this study, basin modeling was employed to investigate the primary source rocks in the Fushan Depression (FD), a significant oil-bearing basin situated in the South China Sea. The research findings indicate that different tectonic zones within the FD underwent distinct hydrocarbon generation stages. The step-fault zone and the central sag zone experienced one hydrocarbon generation stage at 10–0 Ma and 30–0 Ma, respectively. The slope zone, on the other hand, experienced two hydrocarbon generation stages, 40–23.5 Ma and 10–0 Ma, controlled by tectonic movements and heat flow variations. Furthermore, critical times for the process of the petroleum system have been determined based on this work and previous literature. The slope zone in the eastern FD is considered a favorable area for conventional hydrocarbon exploration due to the high maturity of source rocks promoted by volcanic heating and two significant oil charges. The central sag zone is identified as an excellent prospect for unconventional resources because of the substantial retention of hydrocarbons in in-source unconventional reservoirs long after hydrocarbon generation. These findings provide a valuable guide for further exploration.