Abstract: Light oil and gas reservoirs are abundant in the Ordovician marine carbonate reservoir in Shunbei Oilfield, Tarim Basin. This presents a compelling geological puzzle, as ultra-deep reservoirs undergo intense alteration and complex petroleum accumulation processes. A comprehensive suite of geochemical analyses, including molecular components, carbon isotope composition, homogenization temperature of saline inclusions, and burial-thermal history of single wells, was conducted to elucidate the genesis of these ancient reservoirs. Three petroleum filling events have been identified in the study area: Late Caledonian, Hercynian-Indosinian, and Himalayan, through analysis of homogenization temperatures of brine inclusions and burial-thermal histories. Additionally, the oil in the study area has undergone significant alteration processes such as biodegradation, thermal alteration, mixing, evaporative fractionation, and gas invasion. This study particularly emphasizes the influential role of Himalayan gas filling-induced evaporation fractionation and gas invasion in shaping the present petroleum phase distribution. Furthermore, analysis of light hydrocarbon and diamondoid parameters indicates the oil within the study area is at a high maturity stage, with equivalent vitrinite reflectance values ranging from 1.48% to 1.99%. Additionally, the analysis of light hydrocarbons, aromatics, and thiadiamondoids indicates that TSR should occur in reservoirs near the gypsum-salt layers in the Cambrian. The existence of the Cambrian petroleum system in the study area is strongly confirmed when considering the analysis results of natural gas type (oil cracking gas), evaporative fractionation, and gas invasion. Permian local thermal anomalies notably emerge as a significant factor contributing to the destruction of biomarkers in oil. For oil not subject to transient, abnormal thermal events, biomarker reliability extends to at least 190 °C. In conclusion, examining the special formation mechanisms and conditions of various secondary processes can offer valuable insights for reconstructing the history of petroleum accumulation in ultra-deep reservoirs. This research provides a scientific foundation for advancing our knowledge of petroleum systems and underscores the importance of hydrocarbon geochemistry in unraveling ultra-deep, complex geological phenomena.