The performance of positive-ion mode atmospheric pressure chemical ionization linear quadrupole ion trap orbitrap mass spectrometry (APCI LQIT Orbitrap MS) has been compared to that of two-dimensional gas chromatography coupled with positive-ion mode electron ionization time-of-flight mass spectrometry (GCxGC/EI TOF MS) for the analysis of group III heavy base oils. Upon APCI, all compounds were predominantly ionized via protonation. However, protonated alkanes are not stable and predominantly generated [M−H]+ ions via elimination of a hydrogen molecule from the protonated molecule. The high-resolution APCI mass spectra provided elemental composition information for the compounds while low-resolution APCI mass spectra were used for semiquantitative evaluation of the relative amounts of the compounds. Ions corresponding to compounds in seven hydrocarbon classes, i.e., (1) linear and branched alkanes, (2) monocycloalkanes, (3) dicycloalkanes, (4) tricycloalkanes and alkylbenzenes, (5) tetracycloalkanes, (6) pentacycloalkanes, and (7) hexacycloalkanes were identified. On the other hand, the GCxGC/EI TOF MS method enabled the chromatographic separation of most analytes. The measured EI mass spectra were used for the identification of the compounds while the GC peak areas were used for semiquantitative evaluation. The detected compounds were classified into three different hydrocarbon classes, (1) linear and branched alkanes, (2) cycloalkanes, and (3) aromatic hydrocarbons. The (+)APCI LQIT Orbitrap MS method was found to be faster and to provide more information for the larger compounds in the samples. For example, polycycloalkanes were only detected by using (+)APCI MS. However, no aromatic compounds were detected. Data processing was more straightforward than when using the GCxGC/EI TOF MS method. However, the latter method provided more accurate results for aromatic hydrocarbons and small alkanes as the analysis of small alkanes by using (+)APCI MS is limited due to the fact that [M−H]+ ions of small alkanes overlap with alkane fragment ions. Both light and heavy aliphatic and aromatic hydrocarbons were detected by using the GCxGC/EI TOF MS method but not polycycloalkanes. Therefore, these two methods complement each other, and each has different strengths and weaknesses.