Ophiocordyceps sinensishas been used as a traditional medicine or healthy food in China for thousands of years.Hirsutella sinensiswas reported as the only correct anamorph ofO. sinensis. It is reported that the laboratory-grownH. sinensismycelium has similar clinical efficacy and less associated toxicity compared to the wildO. sinensis. The research of theH. sinensisis becoming more and more important and urgent. To gain deeper insight into the biological and pharmacological mechanisms, we sequenced the genome ofH. sinensis. The genome ofH. sinensis(102.72 Mb) was obtained for the first time, with > 99% coverage. 10,200 protein-encoding genes were predicted based on the genome sequence. A detailed secondary metabolism analysis and structure verification of the main ingredients were performed, and the biosynthesis pathways of seven ingredients (mannitol, cordycepin, purine nucleotides, pyrimidine nucleotides, unsaturated fatty acid, cordyceps polysaccharide and sphingolipid) were predicted and drawn. Furthermore, infection process and mechanism ofH. sinensiswere studied and elaborated in this article. The enzymes involved in the infection mechanism were also predicted, cloned and expressed to verify the mechanism. The genes and proteins were predicted and annotated based on the genome sequence. The pathways of several active components inH. sinensiswere predicted and key enzymes were confirmed. The work presented here would improve the understanding of the genetic basis of this organism, and contribute to further research, production and application ofH. sinensis.