The introduction of beneficial bacteria into soil or plants can reduce the occurrence of soil-borne diseases to a certain extent, but the biocontrol effect is often unstable. In order to improve the stability of beneficial bacteria, we used beneficial Bacillus amyloliquefaciens strain QL-18 and Ralstonia pickettii QL-A6 as model strains. We combined two biocontrol methods, which are bio-organic fertilizer containing strain QL-18 and stem injection of strain QL-A6, to investigate efficacy of disease suppression, via greenhouse experiment and two-season field trials (spring and autumn). Furthermore, the potential mechanisms were revealed by comparing the density ratios of beneficial bacteria to pathogen. Results showed that biocontrol efficacy of combined application of bio-organic fertilizer with stem injection was 80.79% in greenhouse experiment, 71.88% in spring field experiment and 81.47% in autumn field experiment, which was significantly higher than single applications in both of greenhouse and field conditions. Single stem biocontrol application and single rhizosphere biocontrol application were less effective in spring and autumn field trials, respectively. And the density ratios of Bacillus spp. to R. solanacearum in the rhizosphere and R. pickettii to R. solanacearum in the stem in combined application were higher than that in single applications. In conclusion, a combination of bio-organic fertilizer and stem injection could be an effective way to enhance suppressiveness against bacterial wilt disease.