Secondary metabolites are considered to be the major compounds in Cordyceps with anti-tumor, anti-aging and immunity-enhancing effects. The molecular structures of secondary metabolites form the basis for the development and utilization of Cordyceps. Metacordyceps neogunnii is an important Cordyceps resource, but less study has been made on the molecular structure of its secondary metabolites. In this study, gas chromatography-mass spectrometry (GC/MS) and ultra performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) were used to analyze and identify the secondary metabolites from CH3OH/H2O extract of Metacordyceps neogunnii. The results show that a total of 22 compounds were identified by GC-MS, including 2 n-alkanes, 1 isoparaffin, 1 cycloalkane, 6 olefins and 13 esters. The predominant compounds were (E)-ocimene, (E)-β-ocimene, methyl oleate, dioctyl adipate, methyl palmitate and methyl linoleate, obtained by means of GC/MS. Five distince classes of secondary metabolites were speculated: 3 polypeptides, 2 esters, 1 isoflavone, 1 isoindrone and 3 amides, from which 10 compounds were detected using UPLC-Q-TOF/MS. (R)-N-((1-(((9H-fluorene-9-yl) methoxy) carbonyl) pyrrolidine-2-yl) methyl)-N-(2-(6-benzoylamino-9H-purin-9-yl) acetyl) glycine, benzyl (5-(2-((3-(2, 3-dihydrobenzo[b] [1, 4] dioxin-6-yl)-4-carbonyl-4H-chromene-7-yl) oxo) acetylamino) amyl) carbamate, 5, 5’-((propane-2, 2-diyl (4, 1-phenylene)) bis (oxo)) bis (2-(naphthalene-1-yl) isoindoline-1, 3-dione), 1-dodecylazepine-2-one and other compounds were the first detected in Metacordyceps neogunnii.