The effect of pretreatment (PT) with Trichoderma sp. AH on the organooxygen compounds (OOCs) in methanol-soluble portions (MSPs) obtained from the methanolysis of raw and pretreated rice straw (RS) was investigated. According to the analyses with a gas chromatograph/mass spectrometer (GC/MS) and negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometer, molecular masses (MMs) of the OOCs range from 100 to 500 u and are dominant from 300 to 450 u. The relative abundances of detected compounds with MMs from 300 to 350 u in MSP of pretreated RS are higher than those in MSP of raw RS. The predominant compounds in MSPs of raw and pretreated RSs are O-n (n = 1-10) with double bond equivalent (DBE) values of 1-28 and carbon atom numbers (CANs) of 4-35. The most abundant classes in MSPs of raw and pretreated RSs are O-5 and O-4, respectively. Besides, N1On (n = 0-9) classes with DBE values of 1-23 and CANs of 4-35 were also identified. These results facilitate understanding the effect of pretreatment with Trichoderma sp. AH on RS conversion and OOC selectivity from the methanolysis of RS and the application of MSP in producing transportation fuel.