Substantial amounts of petroleum were recently discovered in the Carboniferous andesite, tuff, breccia, and basalt reservoirs of the Chepaizi uplift in the western Junggar Basin. However, the charging history of the Carboniferous petroleum reservoir is poorly understood. Oil–oil correlation studies indicate that all of the oils were mainly derived from the middle Permian Wuerhe Formation source rocks, possibly mixed with a small contribution from Carboniferous Baogutu Formation source rocks in the neighboring Changji sag. Based on the petrographic and microthermometry of fluid inclusions, two hydrocarbon charging episodes are defined; these episodes were characterized by a low-peak-range homogenization temperature (Th) distribution (80°C–90°C) and high salinity (13.22–13.42 wt. % NaCl) and a high-peak-range Th distribution (120°C–130°C) and low salinity (4.89–11.72 wt. % NaCl), respectively. Through one-dimensional basin modeling and pressure–volume–temperature–composition simulation, the burial-thermal histories for wells P61, P66, P668, and P663 were reconstructed, and their trapping temperatures of the hydrocarbon inclusions were calculated to be higher than their corresponding highest paleotemperature (i.e., 56.8°C, 53.7°C, 60.9°C, and 58.1°C, respectively), implying fast hydrocarbon charging processes promoted by deep hydrothermal fluids. Associated with the hydrocarbon generation history, sealing process of the Hongche fault, and regional tectonic evolution, these two hydrocarbon charging events were deduced as the adjustments of oils previously accumulated along the Hongche fault zone, because of the tectonic extension in the Paleogene and regional tilting in the Neogene, respectively. The general direction of oil charging was traced from south to north and from east to west, as indicated by the molecular parameters of nitrogen-bearing compounds and C20 + C21 triaromatic steroids/C20 + C21 + C26–C28 triaromatic steroids (TA(I)/TA(I+II)), which roughly coincided with the active fracturing.