The invention relates to cordycepin biosynthetic related genes and application thereof. By adopting a suppression subtractive hybridization (SSH) technique, seven cordycepin biosynthetic related genes which are named as chcs1, chcs2, chcs3, chcs4, chcs5, chcs6 and chcs7 respectively are cloned, wherein the length of cDNA sequence of the chcs2 is 774bp. Through constructing an expression transformative vector of a high-efficiency plant containing the genes, means of biosynthetic gene copy amount in thalli is increased, and the content of cordycepin thalli for expressing cordycepin is improved,so as to meet requirement on medical development.