The Cordyceps are used around the world due to its high medical and pharmaceutical value. Advanced biotechnology has revealed that Cordyceps sinensis has a wide range of secondary metabolites and amino acids. The secondary metabolites and amino acids are very important for the prevention and cure of diseases in human. The purpose of this study was to identify and determine of secondary metabolites and amino acids in Cordyceps. The secondary metabolites were qualitatively determined by gas chromatography mass spectrometer (GCMS). And then, the amino acids were determined by high performance liquid chromatography with fluorescence detection (HPLC-FLD). The secondary metabolites in Cordyceps were found to be cordycepin, octadecanoic acid, ethyl ester, hexadecanoic acid, linoleic acid, d-Mannitol, vitamin A, ecosanoic acid, cholesta, L-lysine, L-Glucose, I-Methionine, oxazolidine, phenylquinoline, adenosine, L-lysine, heptasiloxane, oleic acid and propionic acid respectively. The amino acid concentrations in Cordyceps samples were found to range from 127.43±1.74 to 700.23±1.48 µg/g for tyrosine, 2.014±1.01 to 12.56±1.29 µg/g for valine, 8.57±0.69 to 14.35±1.17 µg/g for iso-leucine and 9.35±0.81 to 18.47±0.88 µg/g for leucine, respectively. Cordyceps contain mainly active compound of cordycepin that have many health benefits and improve immunity on human health. Moreover, other secondary metabolites are mostly present in Cordyceps. The most abundant amino acid is tyrosine and leucine in Cordyceps. Therefore, the regular consumption of Cordyceps can help for human health such as improvement of cardiac functions, lung functions, sexual dysfunctions and immunity.