Objective To explore the investigation method of complicated and profound traditional Chinese herbal medicine,the potential action mechanisms of flavonoids from Scutellaria baicalensis were studied by docking calculation.Methods In total, eight flavonoids (aglycones and their glicosides) from S. baicalensis were selected as ligands.The crystalline structures of targets related to common diseases were used as the receptors for calculation. The calculations were conducted with Schr(o)dinger software package. The grading standard of selectivity was developed according to G-score between ligands and receptors. Results Twenty-six pharmacologic actions have been reported.Among all effects in literature, nine of them can be deduced from the docking calculation of aglycone. From glycosides with grade ++, 25 reported effects can be estimated by calculation. Apparently, the target selectivity of aglycones and their glycosides are different form the virtual evaluation. The virtual evaluation results of glycosides were closer to the reported effects. Conclusion Our proposed virtual evaluation method seems an effective way to investigate the complicated system of traditional Chinese herbal medicine. It suggests that aglycones may be effective as the form of glucoside in vivo, and metabolism is a very important factor for virtual evaluation.