Abstract Conventional one-dimensional gas chromatography-mass spectrometry (GC–MS) has been employed for the organic compound analysis since the 1960s. In traditional GC–MS analysis, co-elution can be intense in the chromatographic region occupied by triterpenoids and aromatic steroids and these can form an unresolved complex mixture (UCM) in the total ion chromatogram (TIC). The UCM in routine GC–MS analysis alters the baseline and adds a substantial noise to mass spectra. Here we demonstrate that comprehensive GC×GC-TOFMS with higher peak capacity helps in an improved characterisation of aromatic hydrocarbon biomarkers by resolving many individual peaks. The use of GC×GC-TOFMS achieved exceptional chromatographic separation of higher plant triterpenoids, triaromatic steroids and methylated 2-methyl-2-(4,8,12-trimethyltridecyl) chromans (MTTC) in a complex aromatic fraction of a Cenozoic crude oil from the Tarapur field of the Cambay Basin. Compounds (e.g., des-A-arbora-5,7,9-triene) having scarce abundance that could not be detected with 1D GC–MS analysis were identified by GC×GC-TOFMS. Thus, this approach offers a new avenue to palaeobiological studies, hydrocarbon exploration and evaluation of the distinct palaeodepositonal environments of organic matter.