The timing of petroleum generation, migration, and accumulation in the central Junggar Basin has been evaluated using basin modeling technology to decipher the processes of petroleum secondary migration and accumulation in the Jurassic carrier beds during the Yanshan and Himalayan orogenies. During the early Yanshan orogeny (J2–J3), crude oils, sourced mainly from the Permian source rocks, migrated laterally from depocenters to adjacent structural high points. During the late Yanshan orogeny (Cretaceous–Eocene), the hydrocarbon secondary migration pattern changed significantly. Specifically, in the Cretaceous, a large-scale regional second phase of generation and migration occurred in the western part of the central Junggar Basin; in the eastern part of the central Junggar Basin, crude oils emplaced in the depressions migrated mainly to the eastern uplifts. In the early Tertiary, oils in the source kitchens generally began migrating to the north and mixed with the Jurassic-generated hydrocarbons. During the Himalayan orogeny (Neogene–Quaternary), this migration was strengthened continually. The modeled results agree with migration-associated geochemical information of the Jurassic accumulations. Integration of the regional geological setting and some petroleum geology data suggest that the Jurassic tectonic high points and facies-change- and unconformity-associated subtle traps are of crucial importance for current oil exploration. Both overpressured bodies in the Triassic and Permian systems and volcanic rock reservoirs of the Carboniferous basement in the uplifts have important implications for future natural oil and gas exploration. This work should help reduce exploration risk in this region.