Combining comprehensive analyses of geological, geophysical and geochemical data and modeling using petroleum system modeling technology, this study tries to restore the evolution processes of organic matter in three sets of Paleozoic shales with no or little drilling data in Petrel subbasin of Bonaparte Basin in Australia. The results show that the entire Permian is the generation peak of Carboniferous shale gas, and the Middle and Late Permian may be the generation peak of oil cracking gas. The shale gas in the Carboniferous Milliigans formation may have been under destruction since the Jurassic, leaving presently limited gas in the shale. The Jurassic is the generation peak of shale gas in the Permian Keyling formation. The shale of Hyland Bay formation in the upper Permian has been at gas generation peak since the Tertiary, and the period since the late Tertiary may be the generation peak of oil cracking gas. Controlled and influenced by regional differential settlement, the source rocks in the middle and north part of Petrel subbasin are deeper with a relatively high degree of organic evolution, while in the east and west part of the basin the rocks are shallower with a relatively low degree of thermal evolution.