Yinggehai Basin is an elongate Cenozoic rift basin on the northwestern margin of the South China Sea continental shelf. Its thick (17 km) basin fill is characterized by high geothermal gradient and high overpressure. Overpressure associated with nonequilibrium compaction mainly occurs at depths more than 2800 m at the basin center and more than 4000 m at the basin margin because the shallow-buried Neogene and Quaternary strata lack effective seals. This regional overpressure distribution, however, is disrupted at basin center where high overpressure occurs in permeable formations at a depth as shallow as 1400 m on top of a series of deep-seated faults and fractures. We studied the processes and mechanisms of overpressuring via numerical modeling that couples basin filling, sediment compaction, and thermal and pressure fields to approach the origin of the shallow high overpressure. Model results indicated that an increase of fluid volume due to natural-gas generation by organic cracking is not large enough to generate the overpressure because of the limited amount of organic matter. The shallow overpressure has probably been generated allogenically. Deep open faults have served as vertical hydraulic conduits and channeled the deep high pressure into shallow permeable formations.