Using the functional strain Bacillus amyloliquefaciens combined with organic fertilizers of different raw materials to prepare different bio-organic fertilizers, the prevention and control of soil-borne bacterial wilt and the promotion of tomato growth, as well as the response of soil nutrients and rhizosphere bacteria to the different bioorganic fertilizers were investigated, to obtain a kind of bioorganic fertilizer that can effectively prevent and control tomato bacterial wilt. B. amyloliquefaciens T-5 was used as a functional strain and was combined with straw organic fertilizer and chicken manure organic fertilizer, the straw bio-organic fertilizer (BIO1) and chicken manure bio-organic fertilizer (BIO2) were prepared through secondary fermentation, then an experiment was conducted in a tomato greenhouse where bacterial wilt is common in Nanjing City of Jiangsu Province. The results showed that both bioorganic fertilizers significantly reduced the incidence of tomato soil-borne bacterial wilt, and the BIO1 had the best prevention and control effect, reducing the incidence by 94.45%. Both bioorganic fertilizers significantly promoted the growth of tomato, increased the biomass of the above ground and the yield of tomato, but did not significantly improve the quality of tomato fruit. In addition, BIO1 significantly increased soil organic matter content, while BIO2 significantly increased soil pH. Soil organic matter had a negative correlation with tomato disease rate and a significant positive correlation with tomato aboveground biomass and yield. High-throughput sequencing analysis found that bioorganic fertilizer significantly increased the bacterial diversity of the rhizosphere meanwhile changed the bacterial community structure. BIO1 had the highest relative abundance of Proteobacteria and lowest relative abundance of Actinomycota. Soil nitrate nitrogen and pH had a significant impact on bacterial communities at the two levels. In conclusion, the straw bio-organic fertilizer prepared with B. amyloliquefaciens as the functional strain and straw as the raw material effectively could prevent and control tomato soil-borne bacterial wilt, and has better effect than chicken manure bio-organic fertilizer. The bioorganic fertilizer could also significantly promote the growth and yield of tomato, improve soil disease suppression and reduce the occurrence of soil-borne bacterial wilt by regulating the relative abundance of the Proteobacteria and Actinomycetes in the rhizosphere bacterial community.