The Bonan sag in the Zhanhua Depression is a prolific oil-producing Cenozoic basin located in the Bohai Bay Basin of China. Three overpressure systems have been identified in the Paleogene Dongying Formation to the first interval of the Paleogene Shahejie Formation, the third interval, and fourth interval of the Paleogene Shahejie Formation, respectively. A combination of drill stem test data, well-log responses, geochemical data of source rocks, basin modeling, and vertical effective stress-density and density-sonic velocity cross plots, were used to investigate the distribution and mechanisms of different overpressure systems in the Bonan sag. The sonic log responds to overpressure development with anomalously high acoustic travel time in the Bonan sag. The Eaton method combined with sonic log data was applied to accurately predict the overpressure magnitude of the three overpressure systems. The overpressure mechanisms differ for each overpressure system. The overpressure in the Dongying Formation to the first interval of the Shahejie Formation, with a top depth from 2000 to 3000 m, is attributed to disequilibrium compaction. The combined mechanisms of disequilibrium compaction and oil generation lead to overpressure in the third interval of the Shahejie Formation with a top depth from 2200 to 3700 m. The overpressure in the fourth interval of the Shahejie Formation, with a top depth from 2500 to 4300 m, is mainly caused by disequilibrium compaction, supplemented by the minor influence of oil generation. Mudstones are the sealing rocks for the overpressure systems in the Dongying Formation to the first interval of the Shahejie Formation and the third interval of the Shahejie Formation. Sealing from the overlying gypsum-rich layer is crucial for overpressure preservation in the fourth interval of the Shahejie Formation. The difference in the oil generation capacity of source rocks and sealing condition controls the variation of overpressure mechanisms in the three overpressure systems in the Bonan sag.