The invention discloses a method for screening anti-androgen activity of flavonoid compounds based on molecular dynamics simulation. The method comprises the following steps: performing butt joint on an optimized tested flavonoid compound structure and a receptor file acquired by homology modeling, then performing molecular dynamics simulation for 20 nanoseconds by using a GROMACS software package, calculating a mean square root deviation of No.12 helix 8-20ns of a flavonoid compound receptor, importing data into a R language package, establishing a distinguishing model for the calculated standard deviation and residues, and removing inactive compounds from the compounds in a fuzzy area by inspecting the movement trajectories of the compounds in the receptor and the calculated mean square root deviation. According to the method disclosed by the invention, quantitative judgment is imported for the first time, the pre-judgment accuracy is improved by the combination of quantitativeness and qualitativeness, the distinction rate of inactive flavonoid and active flavonoid reaches 87.5%, the screening rate of the inactive flavonoid reaches 90%, the laboratory workload can be greatly reduced, the consumption of test products is reduced, resources are saved, and the prediction accuracy of QSAR can also be greatly improved, so QSAR can be really applied.