To study the effects of mixed culture fermentation (MCF) of Bacillus amyloliquefaciens and Trichoderma longibrachiatum on its constituent strains and the application values for agricultural production, with the intention of developing efficient and environmentally friendly biocontrol agents. Methods and results: In this study, an in vitro antifungal growth experiment showed that the inhibitory rate of the MCF broth on pathogenic fungi (Fusarium oxysporum f. sp. lycopersici, Botrytis cinerea, Trichothecium roseum and Colletotrichum gloeosporioides) was less than that of B. amyloliquefaciens culture fermentation (BCF). Moreover, the content and gene expression of lipopeptide antibiotics were also lower than that in the BCF group. However, the pot experiments based on irrigation with appropriately diluted fermentation broth showed that the biocontrol effect of MCF on tomato Fusarium wilt was significantly higher than that of TCF (T. longibrachiatum culture fermentation) and BCF, and was approximately 15.79% higher than that of the BTF group which made by mixing equivalent amounts of BCF and TCF. In MCF broth, two micro-organisms antagonized and coexisted, and the growth of T. longibrachiatum was inhibited. Using transcriptomic analysis, we speculated that MCF can upregulate the expression of genes related to carbon and nitrogen metabolism, oxidation-reduction activity, sporulation, environmental information response and chemotaxis, and biosynthesis of secondary metabolites of B. amyloliquefaciens, which might enhance the nutrient substances metabolism and competitiveness, survival ability, colonization and adaptability to the environment to increase its biocontrol potential. Conclusions: Mixed culture fermentation could promote the more reasonable and effective utilization of biocontrol micro-organisms though improving biocontrol effect, enhancing strains survival and competitiveness, increasing beneficial metabolites, combined with resistance induction or synergistic control. Significance and Impact of the Study: Using MCF agronomically utilizes biocontrol agents in an efficient way, which has a good potential for commercial implementation and could reduce production costs.