The mechanism of biocontrol of plant pathogens by antagonistic bacteria (M3, 1–7 and M2) endogenous in Amorphophallus konjac(A. konjac) was investigated. The results showed that the three strains inhibited a wide range of plant pathogens. The strains and their crude metabolites showed antagonistic effects to Pectobacterium carotovora sub sp.carotovora (Pcc) with different virulence. Three antagonistic bacteria contain different antibiotic genes and have high similarity in nutritional factors with Pcc. Three strains have a long-term colonization in the rhizosphere and in vivo A. konjac with a large number, among which M3 showed the strongest colonizing ability. Inoculation time, inoculum size and method showed a great influence on biocontrol effect which was positively correlated with inoculum size. Inoculation of the antagonistic bacteria 1 day before pathogen inoculation showed the best biocontrol effect. The control efficacy of coating was better than the effect of root watering and the control efficacy of M3 inoculated through coating reached 79.15%. After applying the antagonistic bacteria, utilization of substrate metabolism carbon source and metabolic activity of microbial communities in A. konjac and its rhizosphere soil improved significantly.