Abstract: A randomized block experiment was conducted in micro-plots to study the effects of bioorganic fertilizer mixed with strain AF11b (Bacillus amyloliquefaciens) on the growth of banana plants and the controlling of banana fusarium-wilt disease in different cropping systems. The results show that the effects of the bioorganic fertilization on the growth of banana are not extremely significant in the different cropping systems compared with the chemical fertilization. The disease index is significantly decreased by the bioorganic fertilizer application and intercropping systems. Compared to the control treatment, the combination of the bioorganic fertilizer with intercropping banana and Chinese Leek (Allium tuberosum) shows a good banana resistance to Fusarium oxysporum decreasing disease index by 54.2% after 121 days of transplanting, and at the same time the number of culturable bacteria is increased significantly (p0.05), while the number of Fusarium oxysporum is decreased significantly (p0.05). The correlation analysis show that the number of Fusarium oxysporum is negatively correlated with the number of culturable bacteria (p0.01), while the number of Fusarium oxysporum is positively correlated with disease severity index (DSI) (p0.01).