Unraveling the charge histories of pools with complex petroleum fluid phases is crucial for effective exploration and fluid prediction. Oil and gas samples from multiphase pools in the Tazhong area of the Tarim Basin, China, were analyzed using complementary geochemical (e.g., gas chromatography [GC], two-dimensional GC coupled with time-of-flight mass spectrometry, compound-specific carbon isotope analysis, and pyrolysis simulations) and geological data to better understand their origins and spatial distribution. The integration of these data suggests that the petroleum in these multiphase pools was significantly impacted by various secondary geochemical processes, including oil cracking, thermochemical sulfate reduction (TSR), and gas invasion. Oil and gas in deep Cambrian pools were altered by oil cracking and TSR due to high temperatures of more than 170°C (320°F) at depths of more than 8500 m (27,900 ft), leading to the generation of secondary products, including diamondoids, organosulfur compounds (OSCs), and TSR-altered, H₂S-rich cracking gases. This deep Cambrian gas, with diamondoids and OSCs, dissolved in the vapor phase, migrated upward through strike-slip faults, and invaded previously charged oil pools in Ordovician carbonates, changing the reservoir fluid characteristics and fluid phases. Thus, condensates were formed due to the introduction of excessive deep gas into the primary oil. The amount of gas invasion decreased with increasing distance from the strike-slip faults, thus forming multiphase pools with a spatial distribution pattern. Oil pools near strike-slip faults are more affected by gas invasion than weakly altered volatile oil pools and unaltered oil pools with greater distances away. The oil pools near the faults form condensate pools that show enrichment of H₂S and carbon isotopic fractionation in C₂–C₄ gas components. This study provides new insights into the causal mechanism and distribution of multiphase pools in superdeep strata and has great potential for petroleum exploration in deeply buried Ordovician carbonates in the Tarim Basin.