Abstract: Effects of complex microbial fertilizer on tomato bacterial wilt and soil microbial diversities were studied by agar media test and BIOLOG GN micro-plate culture.Agar medium antagonistic test showed that pure culture of Ralstonia solanacearum were inhibited by compound microbial fertilizer.The pot experiments indicated that the complex microbial fertilizer delayed the disease occurrence time and reduced the disease severity in infested and CK soil,and increased the average well color development(AWCD) and diversity index.The principal component analysis showed that functional diversity of soil microbial community treated with compound microbial fertilizer shift to disease-resistance.The components of carbonhydrate and polymer were prior to utilize by soil microbe,while utilization efficiency of carboxylic was low.