The effects of ecological organic fertilizer (EOF) on tomato bacterial wilt and soil microbial community were studied through field trial and fatty acid methyl esters (FAMEs) analysis. The results showed that the incidence rate of tomato bacterial wilt was 100% in continuous cropped soil, and significantly reduced to 39% and 50% when applying EOF at 1.0 kg.m-2 and 0.5 kg.m-2, respectively. There was no significant difference between two fertilization treatments. The fatty acid fingerprints of soil microbial community were greatly changed, and the relative contents of cyc17:0 cited as biomarker for GN bacteria, c18:2 w6 as biomarker for fungi and c16:1 11c as biomarker for arbuscular mycorrhizal (AM) fungi all increased when applying EOF. The minimum distance of cluster analysis was 1.08 between control and treatments of applying ecological organic fertilizer, and 0.70 between different fertilization treatments. Applying EOF could adjust soil microbial community structure, benefit for soil beneficial microbes, and develop stability and disease suppression of soil ecological system, and hence, improve soil quality.