Cordyceps sinensis, known as DongChongXiaCao (winter worm summer grass) in Chinese because of its appearance during different seasons, is a composite consisting of the stromata of the fungus and the dead caterpillar. The fungus Cordyceps sinensis (Berk.) Sacc. (Fam. Hypocreaceae) is parasitized on the larva of some species of insects (Fam. Hepialidae). According to record of traditional Chinese medicine, Cordyceps sweet in taste and neutral in nature, can replenish the kidney and sooth the lung, arrest bleeding, resolve phlegm, and suppress cough. It is commonly used to replenish the kidney and soothe the lung for the treatment of fatigue, night sweating, hyposexualities, hyperglycemia, hyperlipidemia, asthemia after severe illness, respiratory disease, renal dysfunction and renal failure, arrhythmias and other heart disease, and liver disease. However, to date, scientific studies on C. sinensis are not sufficient to offer understanding of its pharmacological activities and clinical efficacies, while the relationship between the compounds and the pharmacological effects of Cordyceps is still partial unclear. Furthermore, most studies have been performed using cultured Cordyceps instead of natural one because the latter is rare and expensive. Therefore, in order to developed effective quality control method for Cordyceps, systematic chemical separation and several analytical techniques, mainly HPLC-DAD/MS, GC-MS have been applied for the determination of chemical characteristics in natural C. sinensis, while bioassay were used for evaluation the relationship of nucleosides in Cordyceps and its immune activities. The major achievements of this study are summarized as follows: (1) Twelve water soluble compounds of C. sinensis were separated by sequential medium pressure liquid chromatography (MPLC) and preparing high performance liquid chromatography (Pre-HPLC). Two compounds were separated for the first time from Cordyceps sinensis. (2) The lipid soluble compounds of C. Sinensis were studied by using gas chromatography – mass spectrometry (GC-MS). Ten free fatty acids and four sterols were identified and quantified by GC-MS. (3) Three analytical techniques including capillary electrochromatography (CEC), capillary electrophoresis – mass spectrometry (CE-MS) and ultra performance liquid chromatography (UPLC) were developed for the analysis of nucleosides and its related compounds in Cordyceps, which provide alternative techniques for quality control as well as determination chemical characteristics in Cordyceps. (4) A specific quality control method was developed based on the characteristics of natural C. sinensis. Furthermore, liquid chromatography – mass spectrometry (LC-MS) was applied for the determination of nucleotides (the first time identified in Cordyceps), nucleosides and nucleobases in Cordyceps, while the degradation of nucleotides to nucleosides as well as nucleosides to nucleobases in Cordyceps was also studied. (5) Immunological tests of various nucleosides suggested that different compositions and ratios of nucleosides have significantly different effects on the release of cytokines in normal and activated mice macrophage. Therefore, the nucleosides’ variation in natural and cultured Cordyceps may result in their difference in immuno-modulating effects. In summary, the present study broadens the knowledge of chemical compositions in natural C. sinensis. Several nucleosides were proven to be bioactive in Cordyceps, while different compositions and ratios of nucleosides have different pharmacological activities. The method, using different sample preparation methods coupled with the markers of adenosine, inosine, guanosine and uridine, is useful to control the quality of Cordyceps.