A bacterial strain N5, showing strong antagonistic activity against Ralstonia solanacearum was isolated from soil. Strain N5 was primarily identified as Bacillus methylotrophicus based on its biochemical and physiological characteristics and 16S rRNA gene sequence analysis. Strain N5 could produce siderophores, β-1,3-glucanase, cellulase and protease, and also had ability to produce some lipopeptide antibacterial substances. Strain N5 was inoculated into organic fertilizer (pig manure︰amino acid fertilizer = 1︰1) to ferment 4 days to make bio-organic fertilizer. Bio-organic fertilizer was estimated by pot experiment for its biocontrol capacity to tomato bacterial wilt disease. The results demonstrated that application of bioorganic fertilizer could significantly promote tomato growth and increased root activity. Application of bioorganic fertilizer could effectively biocontrol tomato bacterial wilt disease. The control efficiency of treatments in which bioorganic fertilizer was applied only in nursery was higher than that in treatments in which bioorganic fertilizer was applied only in pot soil. Application of bioorganic fertilizer both in nursery and pot soil could much more effectively biocontrol tomato bacterial wilt disease with efficiency of 69%, but common organic fertilizer could not control tomato bacterial wilt disease. Application of bioorganic fertilizer could significantly increase the number of bacteria and actinomyces and reduce the number of fungi and Ralstonia solanacearum in rhizosphere soil compared to control.