Abstract: Banana wilt caused by Fusarium oxysporum f. sp. cubense is one of the most widespread and severe diseases in the world. In recent years, banana-sugarcane rotation plantation has been used to prevent and control Fusarium wilt of banana in some farmlands in the Pearl River Delta with good effects. Banana-sugarcane rotation had been recorded in ancient Chinese book Guangdong New Sight, but the role, control effect and mechanism of the rotation system was unclear. Therefore, the control effect of banana Fusarium wilt after different years of sugarcane rotation was studied and soil micro-ecological mechanism discussed in this paper. The complete random design method with 4 treatments of medium-resistance 'Nongke No. 1' banana and 'Guangdong Yellow Peel' sugarcane were used in the experiment. The farmland with 11 years of continuous cropping of banana (CK) was the control. Other three treatments were continuous cropping of banana ration with sugarcane for one year (GZ1), two years (GZ2) and three years (GZ3) before replanting banana for 1 year. The banana Fusarium wilt disease incidence after various years of sugarcane rotation was investigated, the numbers of soil culturable micro-organisms measured, and soil microbial composition and structure analyzed using the high-throughput DNA sequencing technique. The results showed that that banana Fusarium wilt incidence in banana continuously planting field was 49.15%. After one year of sugarcane rotation, the incidence dropped to 17.86% and the effect of the relative control was 63.66%. After two or three years of sugarcane rotation, the incidence was only 1.79% and the effect of the relative control was above 95%. The amount of cultivable bacteria increased significantly along with increased year of sugarcane rotation, but the amounts of Fusarium oxysporum and actinomycetes significantly decreased. The amount of fungi did not significantly change. Sequence analysis showed that soil bacterial diversity index reduced with the number of years of sugarcane rotation. The relative abundance of bacteria of Pseudomonadales, Planctomycetales, Acidimicrobiales and Solirubrobacterales apparently increased with increasing number of sugarcane rotation years and had significantly negative correlation with the incidence of banana Fusarium wilt. Meanwhile, bacteria of Acidobacteriales, Rhodospirillales, Legionellales and Enterobacteriales apparently decreased and had significantly positive correlation with the incidence of banana Fusarium wilt. In summary, banana-sugarcane rotation significantly reduced banana wilt incidence, compared with continuous banana cropping system. The inhibiting effect apparently increased with increasing number of years of sugarcane rotation. In two years of sugarcane rotation of banana field, the incidence of banana wilt significantly reduced and the yield of banana significantly increased; which was consistent with the results recorded in the Guangdong New Sight. The changes in bacterial community structure in the soil played an important role in the control of banana Fusarium wilt.