The petroleum geological exploration and research in the southern Junggar Basin has been focused mainly on the Permian and Jurassic petroleum systems. In this paper, we reported for the first time general features of the Cretaceous petroleum system, including source rocks, oil sources and petroleum migration/accumulation. The Cretaceous petroleum generation and accumulation center is located in the area from Manas to Hutubi, with the thickest mudstone reaching up to 250 m and best source rock whose organic matter type to Ⅰ—Ⅱ1. The source beds have passed into peak oil window since Paleogene. Their associated oils are occurred mainly in the reservoir sequence from Paleogene Anjihaihe Formation to Cretaceous Tugulu Group. The reservoir filling process can be divided into three stages. During the first stage in Late Pleistocene, the Cretaceous oil migrated and accumulated in the reservoir sequence. Then, during the second stage in Middle to Late Pleistocene, not only the Cretaceous oil, but also the Paleogene source derived oil participated in the migration/accumulation. During the last stage in the end of Pleistocene, the oil/gas, especially the Jurassic source derived gas, remigrated vertically along faults. This complex petroleum migration and accumulation indicates that the Cretaceous petroleum system should be placed enough emphasis in the future petroleum geological exploration and research in the southern Junggar Basin.