Intracratonic strike-slip faults in central-western China's Tarim Basin serve as critical conduits for hydrocarbon migration and accumulation. This study integrates geochemical characterization, in-situ calcite U-Pb geochronology, and fluid inclusion microthermometry to resolve the long-debated temporal relationships between tectonic reactivation and hydrocarbon charging processes in the ultra-deep Shunbei fault system. Through systematic analysis of reservoir oils and fracture-filling calcites from the Shunbei Nos. 4, 6, and 8 fault zones, we establish a novel chronological framework combining differential hydrocarbon accumulation with fault activation phases. Building upon previous structural analyses, our U-Pb geochronology resolves four distinct tectonic phases for the No. 4 fault: Middle–Late Caledonian (473 ± 12 Ma and 443 ± 17 Ma), Late Caledonian–Early Hercynian, Middle–Late Hercynian, and Indosinian–Yanshanian, while the No. 8 fault exhibits four episodes spanning Middle–Late Caledonian (453.5 ± 2.5 Ma, 413 ± 29 Ma) to Indosinian-Yanshanian (196 ± 57 Ma). Hydrocarbon charging occurred through four discrete phases, with No. 8 fault demonstrating earlier petroleum emplacement (principal oil: 294 ± 29 Ma; principal gas: 196 ± 57 Ma) relative to No. 4 fault (principal oil: 282–205 Ma; principal gas: 196–11 Ma). MDR-MPI-1 correlations reveal hydrothermal influence on select oils, causing maturity overestimation. Fluorescence spectra (λmax <445 nm) and geochemical indices (vitrinite reflectance equivalent: 1.2%–1.6%) confirm high thermal maturity. Stable carbon isotopes (δ13C1 < δ13C2) confirm normal genetic oil-type gas with low thermal maturity. Diamondoid indices and gas compositional trends (ln(C2/C3) vs. δ13C2–δ13C3) demonstrate predominant kerogen-derived methane with subordinate oil-cracked contributions. Enhanced vertical connectivity and elevated source maturity in No. 8 fault account for its preferential hydrocarbon enrichment. This work establishes a genetic linkage between multi-phase fault activation and differential hydrocarbon accumulation, providing an innovative methodology for evaluating ultra-deep reservoirs in cratonic basins through coupled geochronological-hydrocarbon fluid inclusion analysis.