Chinese caterpillar fungus is a fungus parasitic on the larvae of Lepidoptera and has been considered to be a precious tonic food and herbal medicine since ancient times in China. its special appearance changing in different seasons. In winter, the larvae were infected by the fungi and turned into worms in soil, which is called Dong-Chong. And in summer, the stroma grew out from the head of the larve like grass, which is why being called Xia-Cao. In China, it has been used in medicine for a long history, dated back to Qing dynasty. Researches indicated that C. sinensis contains many bioactive constituents, such as polysaccharide, adenosine, cordycepin, cordycepic acid, ergosterol and minerals. To date, several fatty acids and amino acids, which are very important bio-functional components, were separated or identified from Cordyceps. GC-MS/MS-based Smart Metabolites Database was employed to establish analysis method for determining 475 metabolites in Chinese caterpillar fungus in the absence of target compounds standard using MRM mode. In the pretreatment process, 2-isopropylmalic acid was added as an internal standard to carry out semi quantitative analysis of metabolites. Through this method, 141 kinds of metabolites in Cordyceps sinensis were identified.