Objective To study the antibacterial components of chloroform and ethyl acetate extracts of the traditional Chinese medicine Artemisia anomala S.Moore. Methods The chloroform and ethyl acetate extracts of Artemisia anomala S.Moore was isolated by silica gel column chromatography. The antibiotic tests of the different isolated fractions in vitro were performed by using Kriby-Bauer method and broth dilution method. The compound structures of the significantly active components were identified by the method of chemical colored-reaction and spectrum analysis. Results Multiple components of chloroform and ethyl acetate extracts of Artemisia anomala had different degrees of antibacterial activities for common pathogenic strains in clinic. The structures of significantly active components were identified as: apigenin, eupatilin, and caffeic acid; eupatilin had the strongest antimicrobial activity for Standard Staphylococcus aureus (ATCC25923) and Standard Staphylococcus aureua (ATCC29213), with the minimal bactericidal concentrations being both 0.062 5 mg/mL. Conclusion The proposed method in the present study is simple and quick; it can accurately and effectively obtain the antibacterial components of the chloroform and ethyl acetate extracts of Artemisia anomala. This study is the first to report the antibacterial activity of eupatilin.