Abstract: The discovery of new drugs from traditional Chinese materia medica and natural products has become the focus in the field of drug research. Although a lot of new compounds could be obtained, it is difficult to identify their targets and conduct investigations on their pharmacological mechanisms due to limited yields. Therefore, structure-based virtual screening, combined with experimental verification of protein biochemistry and pharmacology, could greatly reduce time cost and compound consumption. This review summarized the screening method of natural products by molecular docking, commonly used softwares for virtual screening, databases of natural products, methods of structural biology, protein data bank(PDB), methods of experimental verification, and some successful examples of lead compound obtained from natural products by virtual screening, so as to provide reference for the rapid discovery of active ingredients from natural products.