Cordyceps sinensis, one of the most valuable traditional Chinese medicines, is a composite consisting of the fungus stromata and dead caterpillar. The amount of C. sinensis is decreasing as the result of environment destruction and the increasing human activities. However, the market demand of C. sinensis is increasing due to the discoveries of numerous pharmacological activities and the awareness of significant health-promoting effects. Therefore, C. sinensis strain cultivation or the development of Cordyceps substitutes should be performed to compensate the drawbacks when available C. sinensis resources become limited in nature. The dissertation can broadly be divided into three sections: (1) The variation strains isolated from C. sinensis were compared basing on morphological identification, molecular approaches, polysaccharides analysis and immunoregulatary effect investigation. Polysaccharides isolated from strain A1 had the highest immunoregualtary effect than that from other strains. Therefore, it is valuable to further investigate the A1 strain. (2) The fermentation conditions and medium were investigated to obtain hyper-bioactive polysaccharides from Cordyceps sinensis fungus UM01. The optimal medium was composed of glucose 30 g/L, sucrose 30 g/L, KH2PO4 1 g/L, CaCl2 0.5 g/L, yeast extract 3 g/L, and MgCl2 0.1 g/L. Under these optimal conditions, the yield of bioactive polysaccharides reached the maximum amount (486.16±19.60 mg/L). It is helpful to establish an efficient and controllable fermentation process for the industrial production of bioactive polysaccharides from C. sinensis UM01. (3) To gain dynamic insight into bioactive markers within the fruiting body growth of Cordyceps militaris on Bombyxmori (B. mori), the samples from different growth stage were collected and analyzed using the HPLC-DAD-ELSD. The result indicated that the trend of nucleosides and carbohydrates was different with the fruiting body formation. And C. militaris cultured on the 5th star silkworm larva for 33 days could accumulate most cordycepin (13.43 mg/g). This study is very beneficial to increase the understanding of Cordyceps sinensis. In summary, strains screening, culture conditions optimization and dynamic analysis between the relationship of markers and the growing status of fruiting body are very important for develop a unique healthy and functional product from Cordyceps and related fungi in future.