The specificity and conversion of supercritical methanolysis of wheat straw (WS) and rice straw (RS) can be enhanced by Pretreatment using Trichoderma sp. AH, particularly the esters of the methanol-soluble portion (MSP) of WS and RS in supercritical methanolysis. However, only about 100 organic compounds of lower volatility and polarity could be detected in MSP by gas chromatography-mass spectrometry. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry was used to determine the organic nitrogen compounds (ONCs) in the MSPs from supercritical methanolysis of raw and pretreated WS with Trichoderma sp. AH. The most prevalent ONCs in the MSPs of native and pretreated WSs in the positive ion mode would be N2On (n = 1–9) species having twin-bonding equivalence values (2–25) together with carbon-atom numbers of 4–35. Peak prevalent ONC within prior-treated WS MSPs is N2O4, with the most abundant ONC in raw WS MSPs is N2O5. These results help to understand the impact of Trichoderma sp. AH pretreatment upon converting ability/specificity for ONCs within WS methanolysis and employing MSP in producing jet fuel.