The total fatty acids and low molecular weight components were determined from four wild edible mushrooms (Tuber aetivum, Cantharellus cibarius, Boletus edulis, and Tricholoma matsutake). The fatty acids were investigated by gas chromatography-mass spectrometry (GC-MS), and the low molecular weight compounds were identified by liquid chromatograph-mass spectrometry (LC-MS) combined with multivariate statistical analysis. A total of 32 fatty acids were detected. The total fatty acids content was the highest in Tub. aetivum. Linoleic acid was the highest in the four wild edible mushrooms. Besides, a total of 144 and 91 differential with 40 mutual low molecular weight compounds were identified in positive and negative ion modes, respectively, mainly including amino acids, organic acids, sugars, and vitamins. Comprehensive multivariate statistics showed that betaine, choline, and 13 other compounds were differential low molecular weight compounds of the four wild edible mushrooms. These results expand our knowledge of the nutrition and flavour precursors in wild edible mushrooms.