Ultra-deep (7300 m–8900 m) condensed and volatile oil reservoirs have been discovered in the Ordovician reservoirs of the Shunbei oilfield, in the Tarim Basin. This study describes the petroleum accumulation process in the Shunbei oilfield by combining an analysis of its geochemical characteristics with seismic section observations and an analysis of petroleum filling events. Geochemical techniques are used to determine the sources, maturity, secondary processes, accumulation periods, and timing of petroleum filling. Analysis of fluid inclusion homogenization temperatures and burial-thermal histories indicates distinct petroleum filling events. Specifically, the north sub-section of the No. 5 fault zone experienced two petroleum filling periods during the late Caledonian and Indosinian epochs while the No. 1 fault zones and the mid-south sub-sections of the No. 5 fault zones experienced three distinct filling periods, encompassing the late Caledonian, Indosinian, and Himalayan periods. The CO2 concentrations and δ13CCO2 values suggest the presence of secondary microbial gases, primarily thermogenic gases. Gas component analysis reveals a transition from kerogen degradation gas to oil cracking gas from north to south. The detection of intact n-alkanes and compounds of the 25-norhopanes series in oil samples suggests a mixture of early biodegradable oil with late fresh oil in the area. Seismic sections reveal diabase intrusions with strong axial reflections. Local hydrothermal activities during the Permian era rapidly cracked saturated hydrocarbon biomarkers, forming polycyclic aromatic hydrocarbons in the oil. Hydrothermal activity in the south sub-section of the No. 5 fault zone depleted the hydrocarbon-generating capacity of the underlying source rocks. Petroleum charged during the Indosinian period likely originated from potential petroleum reservoirs in the Cambrian system. This explains the comparatively low temperature of the SHB57X reservoir (163.32 °C) and the lack of strong hydrothermal activity in the late stage, but no biomarkers of the second-stage charged oil have been detected. Biomarker detection and gas genesis in the mid-south sub-section of the No. 5 fault zone and in the No. 1 fault zone suggest weak or no hydrothermal activity, with Cambrian source rocks maintaining their hydrocarbon generation capacity. Gas filling in the Himalayan period caused evaporative fractionation in the original reservoirs, resulting in a disproportionate (2-MH+2,3-DMP)/(3-MH+2,4-DMP), producing high K1 values in the light hydrocarbons in the present petroleum reservoirs. Differences in gas charging events in the Himalayan period led to the present distribution of petroleum phases.