Abstract: The reservoired petroleum fluids in the deep Ordovician carbonates in the Tazhong area, Tarim Basin, exhibit diverse and intricate geochemical properties and petroleum phases. However, the study on the causal mechanisms for the genesis of co-existed complex petroleum phases and their distribution remains relatively limited. The quantitative assessment of changes in molecular compounds in petroleum pools influenced by secondary alteration to different degrees also needs further investigation. In this study, eight samples including condensate, volatile, and black oil from the Tazhong area were analyzed via GC × GC-TOFMS. The results reveal that condensate oil exhibits complete normal alkane distribution, with abundant diamantanes and organic sulfur compounds (OSCs), and features high density (>0.83 g/cm3), elevated wax content (>20%), and remarkable gas washing loss. The condensate gas is characterized by highly mature oil-cracking gas with a heavy carbon isotope. Geological analysis indicates that the current Ordovician reservoir temperatures generally remain below 140 °C, which is insufficient to induce in-situ oil cracking. Additionally, black oil pools are formed adjacent to the condensate gas pools, suggesting that the latter is not a result of in-situ oil cracking, but rather represents a secondary condensate gas pool formed through gas invasion of a pre-existed oil pool. Based on the loss of n-alkanes and variations in adamantanes (As) and diamantanes (Ds) content across different oil samples, the degree of gas invasion was assessed. We divided gas invasion intensity into strong (Q ≥ 80%, As≥5000 μg/g, Ds ≥ 400 μg/g), weak (20% ≤ Q < 80%, 3000 μg/g ≤ As < 5000 μg/g, 200 μg/g ≤ Ds < 400 μg/g) and negligible (0 ≤ Q < 20%, As < 3000 μg/g, Ds < 200 μg/g). The multistage oil/gas charging events, specifically the sequence of “early oil and late gas” in the Ordovician from the Tazhong area, predominantly drives the phase evolution of reservoired petroleum. Furthermore, differential gas invasion alteration exacerbates the intricacy of petroleum phase distribution. Notably, gas washing processes significantly influence the disparate enrichment of diamondoids homologues in crude oil. Specifically, lower carbon number diamondoids are more abundant in condensate oil, while higher ones exhibit relatively increased abundance in black oil, potentially serving as a valuable quantitative assessment parameter. The findings in this study will provide guiding significance for the analysis and quantitative assessment of deep petroleum phase diversity. Additionally, this research will provide novel insights for comprehensively evaluating basins worldwide with complex petroleum phases distribution.