The Yinggehai Basin is a strongly overpressured Cenozoic basin developed in the northern continental shelf of the South China Sea. The flow of overpressured fluids in this basin has given rise to strong effects on petroleum accumulation. (1) The overpressured fluid flow has enhanced the maturation of shallow-buried source rocks, which has caused the source rocks that would have remained immature under the conduction background to be mature for hydrocarbon generation. As a result, the overpressured fluid flow has increased the volume and interval of mature source rocks. (2) The overpressured fluid flow has strong extraction effects on the immature or low-mature source rocks in the shallow parts. This has increased, to some extent, the expulsion efficiency of the source rocks. More importantly, the extraction effects have strongly limited the effectiveness of biomarker parameters from oil and condensate in reflecting the source and maturity of the oil and gas. (3) The flow has caused the sandstones in the shallow parts to get into the late diagenesis stage, and significantly reduced the porosity and permeability of the sandstones. This study confirms that even in sedimentary basins in which no topography-driven groundwater flow systems have ever developed, the cross-formation migration of overpressured fluids and the resultant energy conduction and material exchange can significantly affect the thermal regime, source rock maturation and sandstone diagenesis. As a result, the effects of overpressured fluid flow must be taken into account in analyzing the mechanism of petroleum accumulation.