Target protein (pharmacophore matching protein) of cordycepin and cordycepin triphosphate were predicted using the reverse molecular docking method of idTarget and PharmMapper online servers. Ledock, molecular docking software was used for simulating the combined conformation of cordycepin and cordycepin triphosphate with target proteins. Software LigPlus was employed to analyze the interaction between the activity pocket residues with ligand of combined conformation. The molecular simulation combined conformation showed that the free combination of cordycepin triphosphate and target proteins was lower than those of cordycepin. The result of molecular docking showed that more hydrogen bonds were formed by amino acid residues from cordycepin triphosphate and target proteins activity pocket. The combined conformation was much stable with the presence of target proteins, and the geometric match between cordycepin triphosphate and target proteins was better as lower free combination energy compared to cordycepin. The cordycepin triphosphate was supposed to be the substance exerted biological activity when cordycepin entered into human body. Hence, we could draw the conclusion that triphosphate cordycepin was the main material with biological activity.