The saturated and aromatic hydrocarbon fractions of crude oil samples have been analyzed by using comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (GC×GC-TOFMS) and conventional gas chromatography-mass spectrometry (GC-MS). In order to investigate the consistency and discrepancy of the obtained data from the two instruments, some petroleum geochemical parameters have been compared. A comparison of 23 geochemical parameters indicates that 10 parameters are comparable from the two instruments with less than 5% deviations. Therefore, GC×GC-TOFMS is equivalent to conventional GC-MS in some geochemical parameter acquisitions. However, the other 13 parameters are discrepant, including gammacerane / αβ-hopane, Ts/Tm, 2-ethyl-naphthalene / 1-ethyl-naphthalene (ENR), (2, 6-dimethyl-naphthalene +2,7-dimethyl-naphthalene) / 1,5-dimethyl-naphthalene (DNR), etc. Furthermore, compared to GC× GC-TOFMS, some low concentration compounds could not be detected by the conventional GC-MS, which results in the missing of related geochemical data. Normally, this is caused by the limited separation power and peak capacity of the conventional GC column. Besides, the co-eluting peak integrations are also affected significantly due to the incomplete separation of the compounds. Some low concentration compounds might not be detected because of the interference from the baseline noise or from other substances. GC×GC-TOFMS prevails in compound separation against the conventional GC-MS by avoiding co-elution, which achieves more accurate and precise peak area measurement with the presence of a true baseline. So petroleum geochemical parameters obtained from the GC×GC-TOFMS are more reliable than those from the conventional GC-MS. GC×GC-TOFMS may become one of the most effective analytical tools for the oil and gas geochemical study. The saturated and aromatic hydrocarbon fractions have been analyzed by using two-dimensional gas chromatography with time-of-flight mass spectrometry (GC × GC-TOFMS) and conventional gas chromatography-mass spectrometry (GC-MS). In order to investigate the consistency and discrepancy of the obtained data from the two instruments, some petroleum geochemical parameters have been compared. A comparison of 23 geochemical parameters indicates that 10 parameters are comparable from the two instruments with less than 5% deviations. Therefore, GC × GC-TOFMS is equivalent to conventional GC-MS in some geochemical parameter acquisitions. However, the other 13 parameters are discrepant, including gammacerane / αβ-hopane, Ts / Tm, 2-ethyl-naphthalene / 1-ethyl- Dimethyl-naphthalene / 1,5-dimethyl-naphthalene (DNR), etc. Furthermore, compared to GC × GC-TOFMS, some low concentration compounds could not be detected b the conventional GC-MS, which results in the missing of related geochemical data. Normally, this is caused by the limited separation power and peak capacity of the conventional GC column. Besides, the co-eluting peak integrations are also affected significantly due to the incomplete separation of the compounds. Some low concentration compounds might not be detected because of interference from the baseline noise or from other substances. GC × GC-TOFMS prevails in compound separation against the conventional GC-MS by avoiding co-elution, which achieves more accurate and precise peak area measurement with the presence of a true baseline. So petroleum geochemical parameters obtained from the GC × GC-TOFMS are more reliable than those from the conventional GC-MS. GC × GC-TOFMS may become one of the most effective analytical tools for the oil and gas geochemical study.