By the use of drilling pressure monitoring data, pressure and interval transit time measured with wireline test, the abnormal overpressure widely developed in the Tertiary of the southern Junggar Basin was identified. The overpressure systems in the worked area can be divided into two types, which were mainly caused by disquilibrium compaction, sealing and tectonic uplift. The abnormal overpressure had a significant control on hydrocarbon accumulation. The overpressure system in Hutubi area of Junggar was benefit for the formation and conservation of gas pools. However, the overpressure system in Dushanzi area was only benefit for the seal and preservation of oil and gas migrated in the same period or before the formation of overpressure system and had a resistance to the later migration of oil and gas towards the overpressure system.