Ultra‐deep marine carbonate reservoirs is an important field for oil and gas exploration, and it is also a hot research topic in recent years. However, their hydrocarbon episodic charging model is still under debate up to now. A great breakthrough has been made in the newly discovered ultra‐deep fault‐karst oil reservoir in the Shunbei area of Tarim Basin. Based on quantitative gas chromatogram‐mass spectrometry, stable carbon isotopes of reservoir oils, microthermometry and confocal laser scanning analyses of fluid inclusions, the reservoir oil origin and hydrocarbon charging history in Shunbei No. 1, No. 5 and No. 7 strike‐slip fault zones are expounded. The results showed that the Ordovician reservoir oil derives from the source rocks within the Cambrian Yuertusi Formation deposited in a highly anoxic bottom water environment. There were four stages of hydrocarbon charging in the study area, in the late Caledonian, late Hercynian–Indosinian, middle Yanshanian and late Himalayan. During this period, the force‐field strength of the charged oil gradually decreased, and the early‐stage charged crude oil with low maturity and high force‐field strength preferentially accumulated in the Yijianfang Formation, while the late‐stage charged crude oil with high maturity and low force‐field strength preferentially accumulated in the Yingshan Formation. This study reveals the history and differences of petroleum accumulation in the Shunbei fault zones, which is significance for understanding the hydrocarbon distribution in ultra‐deep marine carbonate reservoirs.