A dominant endophytic fungus（MS-01） isolated from the root of ginseng was identified and its antimicrobial activity was studied. The methods of morphological observation and molecular biology were used. The strain was identified as Chaetomium subaffine. The results of the confrontation culture and the bacteriostatic test of fermentation broth showed that the strain had a good inhibitory effect on ginseng root rot fungus, and the bacteriostatic rate was（61.57±0.68）%. At the junction of the strain and ginseng root rot fungus, the mycelia of ginseng root rot bacteria dissolved and broke. The bacteriostatic rate of unsterilized MS-01 fermentation broth against ginseng root rot was（79.92±0.77）%.The bacteriostatic rate of sterilized MS-01 fermentation broth against ginseng root rot was（47.22±0.39）%. The results of indoor potted experiment showed that the strain had a certain control effect on ginseng root rot. This study provides a theoretical basis for biological control of ginseng root rot.