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Large amounts of processing tomato are grown in Xinjiang, China. Tomato black spot disease, caused by <i>Alternaria</i> spp., and the produced alternaria toxins in tomato products are posing risks to human health. In this study, we isolated a rhizospheric bacterium, XJ-BV2007, from tomato (<i>Solanum lycopersicum</i>) fields, which we identified as <i>Bacillus amyloliquefaciens</i>. We found that this bacterium has a strong antagonistic effect against <i>Alternaria alternata</i> and reduces the accumulation of alternaria toxins in tomatoes. According to the antifungal activity of the bacteria-free filtrate, we revealed that <i>B. amyloliquefaciens</i> XJ-BV2007 suppresses <i>A. alternata</i> by the production of antifungal metabolites. Combining semi-preparative high-performance liquid chromatography, we employed UPLC-QTOF-MS analysis and the Oxford cup experiment to find that fengycin plays an important role in inhibiting <i>A. alternata</i>. This paper firstly reported that <i>B. amyloliquefaciens</i> efficiently controls tomato black spot disease and mycotoxins caused by <i>A. alternata</i>. <i>B. amyloliquefaciens</i> XJ-BV2007 may provide an alternative biocontrol strain for the prevention of tomato black spot disease.