The present invention relates to an HPV infection-resisting pharmaceutical composition and an application thereof, and belongs to the technical field of medicine and health. The composition is mainlyprepared from a radix arnebiae pulverized material, a cortex phellodendri amurensis pulverized material, a radix astragali pulverized material, etc., and can be prepared into powder, tablets, capsulesor ointment. The other composition is prepared from a radix arnebiae alcohol extract, a cortex phellodendri amurensis water extract, a radix astragali water extract, then propylene glycol, deionizedwater, antimicrobial peptides, etc., and can be prepared into suppositories, gels, lotions, foaming agents or ointment. Through synergistic effects of the various raw materials, the HPV infection-resisting pharmaceutical composition has effects of clearing heat, eliminating dampness, removing toxins and blood stasis and enhancing body immune functions, effectively inhibiting and eliminating HPV viruses and also preventing inflammation, can obviously prevent re-infection of the HPV viruses, can be used for preventing and treating clinical symptoms caused by HPV infection, particularly common warts, flat warts, vulvar cancer, anal cancer, cervical cancer, etc.