. Fusarium oxysporum is a soil-borne fungus that infects soybean roots and causes soybean root rot, a widespread and destructive soybean disease. The potential strain X6 belonged to Bacillus subtilis for controlling soybean root rot. And antagonistic mechanism of the pathogenic Fusarium oxysporum of soybean root rot by B. subtilis X6 was investigated. The antagonistic mechanism of strain X6 againt F. oxysporum can effectively inhibit mycelial growth, spores bearing and germination. After treated with metabolic product of strain X6, protoplast from the hyphae became abnormal. The activity effect of metabolic product of strain X6 was sensitive to temperature. So the study lay the groundwork for further research and application.