In recent years, newly discovered ultra-deep fault-karst reservoirs in the Shunbei area of the Tarim Basin have greatly increased the prospectivity of the basin and become a hotspot for further hydrocarbon exploration. In this study, the diagenetic sequences of the Lower-Middle Ordovician reservoir were established through observation of thin sections under transmitted light, reflected light, and cathode luminescence. The hydrocarbon charge history in the Shunbei area was reconstructed and associated with a series of diagenetic events using fluid inclusion microthermometric measurements combined with one-dimensional basin modeling. The results show that the Shunbei area has experienced three hydrocarbon charging episodes in total, in the late Caledonian, late Hercynian, and late Himalayan. Finally, the relationship between measured QF-535 factors and the API gravity of crude oil was used to quantify the level of contribution of each of the petroleum charging episodes to the No. 1, No. 5, and No. 7 fault zone reservoirs. The contribution of early hydrocarbon charging episodes gradually increases from west to east in the Shunbei area. This increase was driven by different tectonic events throughout geological history and the subsequent evolution of paleo-structural patterns. This study has a significant impact on marine carbonate reservoir evaluation in strike-slip fault zones in China.