Microbial confrontation is ubiquitously present in nature, such as mycoparasitism, competition and antibiosis between biocontrol agents and microbial pathogens. However, the internal metabolic responses of fungal pathogens under microbial interaction scenario have been scarcely investigated. In this study, we set up an integrated mycotoxin analysis and non-targeted metabolomics workflow to decipher metabolic changes of Alternaria pathogens when confronted with selected Trichoderma strains, as well as mycotoxin metabolization in the Trichoderma spp. Results demonstrated that Trichoderma spp. significantly influenced mycotoxin production and whole metabolome of Alternaria pathogens when in cocultivation, and one Trichoderma strain could metabolize alternariol into its hydroxylated form. These differential metabolites revealed fungal physiological alternations in various confrontation conditions. In all, a MS-based strategy was proposed to investigate microbial metabolic profiles under fungal/fungal and fungal/mycotoxin cocultivation, and this generic methodology would be significant for understanding the occurrence and change of food contaminants in microbial interactions.