Abstract: An endophytic fungi strain Y18, the metabolites of which had good antimicrobial activities, was isolated from Eucommia ulmoides Oliv and the antimicrobial mechanism of its metabolites was also studied. The effects of the metabolites of the endophytic fungus strain Y18 on E. coli cell membrane and the structure of the protein and DNA were studied by flow cytometry (FCM) and fourier transform infrared spectroscopy (FT-IR) . Results showed that, after the treatment of the metabolites, the cellular membrane permeability of E. coli cells was increased and the structure of the protein and DNA were changed. The relative electric conductivity of E. coli was 16. 22% and the percentage of PI-stained E. coli reached 25. 31% after 4 hours. The β-fold structure increased from 34. 60% to 41. 47%. Meanwhile the proportion of α-helix, random coil and β-turn reduced. Among them, the random coil structure dropped obviously from 21. 80% to 18. 67%. The structure of nucleic acid materials had also been changed.