Recently, considerable hydrocarbon reserves have been discovered in Lower–Middle Ordovician carbonate reservoirs situated surrounding two conjugate strike-slip fault zones in the Shunbei oil field, Tarim Basin, northwestern China. Through the integrated analysis of crude oil physical properties, geochemical compositions, and fluid inclusions, the differential petroleum charging history of the Shunbei oil field has been investigated. For the Shunbei (SHB)5 fault zone, two discrete ranges of homogenization temperature of coeval aqueous inclusions indicate intense charging during the early Yanshan Orogeny, with minor charging during the late Himalayan Orogeny. For the SHB1 fault zone, the extended homogenization temperature range probably reflects continuous charging from the early Yanshan to the late Himalayan Orogenies. The presence of bitumen indicates an earliest petroleum charging event during the late Caledonian Orogeny. Differential petroleum charging during the Himalayan Orogeny caused stark differences in the thermal maturity of trapped oil and the mixing of oil with variable maturity, with the SHB1 fault zone receiving more intense charging of late-stage oils than the SHB5 fault zone. The differential petroleum charging during the Himalayan Orogeny can be explained by preferential reactivation of northeast-trending strike-slip faults, controlled by the regional northeast 45°-oriented compressive stress field. Crude oil with high maturity would preferentially migrate vertically via the reactivated northeast-striking SHB1 fault zone, charging into reservoirs, resulting in the current maturity differences in the trapped oils in the Shunbei oil field. These results illustrate the preferential vertical petroleum migration along the reactivated fault and the controlling role of the regional stress field on fault behaviors.