Biological control agents and soil amendments have been applied to control tobacco bacterial wilt, but the mechanism is not well-known. In the present study, a field experiment was performed to investigate the soil physicochemical properties, disease index (DI) and disease incidence of tobacco bacterial wilt, and rhizosphere microbial community. The results show that the control efficacy of single application of antagonistic bacteria and calcium cyanamide was 46.43% and 51.92%, respectively. While the combined control efficacy of antagonistic bacteria and calcium cyanamide was 65.79%. Besides, the combined application of antagonistic bacteria and calcium cyanamide could increase soil pH, total N alkaline N, and exchangeable Ca, which were negatively associated with the microbial diversity, soil-borne pathogenic microorganisms, and incidence of tobacco bacterial wilt. Additionally, the combination of antagonistic bacteria and calcium cyanamide can improve the proportion of some antagonistic microbial species, and these antagonistic microbial species were inversely associated with the DI of tobacco bacterial wilt. In conclusion: The integrated measure may influence soil microbial communities through enhancing soil physicochemical properties and rebuild healthy soil microbial community structure to mitigate tobacco bacterial wilt. The current study presented valuable insights into the mechanisms enhancing soil health in the integrated measure.