The control effect of banana Fusarium wilt(Fusarium oxysporum f. sp. cubense, Foc)by bio-fertilizer (F), chitosan degrading liquid (C), hymexazol (H) and their combinations was studied. The soil bacterial community diversity was investigated by Biolog Eco plate and T-RFLP techniques under pot experiment. The results showed that banana Fusarium wilt index in the treatment of the combination of bio-fertilizer and hymexazol (H+F) was the highest, and the lowest in the combination of bio-fertilizer and chitosan degrading liquid(C+F), compared with the sterilized bio-fertilizer treatment(CK). The control effect of C+F treatment was 42.0%, higher than that of single bio-fertilizer (32.8%). However, The treatment of H+F increased the severity of Fusarium wilt. The average well color development (AWCD) in Biolog plate indicated the ability of carbon utilization of microbial communities, while the indices of Shannon, Smipson and McIntosh were calculated to show the richness, dominance and evenness of the functional diversity. The changes of AWCD and diversity indices (including to Shannon H, Simpson D, Mcintosh U) were negatively correlated with the control effect in different treatments. The better effect of controlling disease showed the lower microbial diversity indices in soils, which further studied by the comparison of AWCD in three samples, including the soil (S), banana pathogenic fungi (Foc) and the mixture of soil and banana pathogenic fungi (S+Foc) by Biolog Eco plate and bacterial identification plate (patent publication number: CN101200755). The results suggested that the pathogenic fungal Foc utilized some carbon substrates well in two plates, which interfered the final color reaction. Therefore, the type and population of pathogens may be considered in the determination of the soil bacterial community functional diversity by Biolog plate. T-RFLP results demonstrated that the number of terminal restriction fragments (TRFs) was the lowest in CK treatment, and the highest in C+F, which meant the better effect of controlling disease with the higher soil bacterial genetic diversity. Compared T-RFLP information with database on the website, the soil bacterial communities traits in the treatments of C+F and F contained the more Bacillus species (the numbers were 17 and 15, respectively) than H+F and CK (3 and 4, respectively) in soil, which implied that the more Bacillus species could be used as effective functional microbes on controlling banana Fusarium wilt. The Biolog and T-RFLP shared the same distribution characteristics by the loadings of principal component analysis (PCA) in treatments, F and C+F were nearer in the space. The combination of bio-fertilizer with chitosan degrading liquid, a kind of bio-pesticides, could effectively control banana Fusarium wilt by enhancing the soil bacterial diversity and improving the community structure, especially the changes of population and diversity of Bacillus spp.