[Background] There are many studies on the use of antagonistic bacteria to control crop diseases, but there are few studies on the effects of secondary metabolites of antagonistic bacteria on cotton rhizosphere soil microbial community. [Objective] To investigate the effects of Verticillium dahliae resistant metabolites of Bacillus subtilis J-15 on the diversity of soil fungi in cotton fields, and to evaluate the ecological security of soil microorganisms for controlling Verticillium wilt of cotton with Bacillus subtilis J-15 and its secondary metabolites. [Methods] The cotton field in Manas area of Northern Xinjiang was selected as the soil sampling point, and 10 sampling points were randomly selected for mixing. After treated with the substance that secondary metabolites of Bacillus subtilis J-15 against Verticillium dahliae for a certain time, the total DNA of soil sample was extracted, and then the ITS1?ITS2 region of fungi in the samples was used to sequence by Illumina Hiseq high-throughput technology, and the effects of the secondary metabolites of Bacillus subtilis J-15 against Verticillium dahliae on the diversity of soil fungi were analyzed. [Results] At the 97% similarity level, the OTU number, Chao1 and ACE abundance index of fungi in the samples after 10 and 30 d of treatment were higher than those of the untreated control group at the same time, while Simpson index was significantly lower than that of the control group. From the community composition analysis, compared with the control group, the relative abundance of dominant fungi in Ascomycota and Mortierellomycota, such as Mortierella and Tricharina, was significantly increased in soil samples treated with secondary metabolites of J-15, while the abundance of Verticillium and Fusarmm, which were higher than 1%, were significantly lower. [Conclusion] Secondary metabolites of J-15 resistant to Verticillium dahliae had significant effect on soil fungal community and abundance in farmland, but did not change the structure of soil fungal community affecting agricultural production.