[Background] Metacordyceps neogunnii was a kind of new resource with the potential application value because it possessed multiple pharmacological functions. However, more active compounds were still worthy of exploring. The research of its active compounds mainly focused on macromolecular or polar compounds up to date, few studies were paid to micromolecular or weak-polar compounds. [Objective] The non-polar or weak-polar small molecular compounds of the petroleum ether extracts from M. neogunnii were researched in this study, in order to improve the chemical fingerprint database of the active substances in the M. neogunnii. [Methods] M. neogunnii were extracted with petroleum ether by soxhlet extraction. The substance components were identified and analyzed by fourier transform infrared spectrometry (FTIR) and gas chromatography-mass spectrometry (GC-MS). [Results] According to FTIR, the analyses found that the components of extracts included the functional groups such as C?H, C=O, C?O and C=C; Through GC-MS method, 109 compounds including alkanes, arenes, olefins, acids, esters, alcohols, amines and others were identified. The non-polar or weak-polar small molecular compounds such as steroids, aromatics, alkanes, amides, olefins and phenols were discovered for the first time; And the relative contents of linoleic acid and its isomer were the highest, up to 38.33%. [Conclusion] Many small active components from M. neogunnii were obtained by petroleum ether extraction, which supplemented the chemical composition and provided scientific data for high value-added utilization of M. neogunnii.