In this study, real time PCR and MiSeq sequencing technology was used to deeply compare the differences of bacterial community structures and compositions in bulk and rhizosphere soils of healthy and diseased tomato-planting fields under mono-cropping system. The results showed that healthy bulk soil displayed higher pH value and total carbon content. The bacterial structures and compositions in healthy bulk and rhizosphere soils were obviously different from those of diseased ones. Compared to diseased rhizosphere soil, healthy rhizosphere soil exhibited a significant higher number of total bacteria and a significant lower number of R. solanacearum. Also, healthy rhizosphere soil showed a significant higher index of Shannon diversity. Furthermore, the relative abundance of Bacteroides and Chitinophaga, Chryseobacterium, Dyadobacter, Flavobacterium and Taibaiella included in Bacteroides was significantly enriched while the relative abundance of Proteobacteria and Ralstonia included in Proteobacteria was significantly depleted in healthy rhizosphere soil compared to diseased one. In summary, soil suppressive to tomato bacterial wilt disease harbored a unique bacterial community, which showed high bacterial population, diversity and relative abundance of beneficial indigenous microorganisms and low relative abundance of pathogen. This research could provide a guideline and theoretical principle for biological control of tomato bacterial wilt disease.