The method of anaerobic soil disinfestations (ASD) involving incorporation of organic matters under flooding condition was used for creating soil anaerobic and reductive environment and controlling the pathogen Fusarium oxysporum (FOC) in banana continuous cropping soils. The results showed that ASD significantly increased soil pH, reduced soil Eh and the concentration of NO3–-N in the soil. In ASD process, the population of cultural bacteria significantly increased, but the populations of antinomies and fungi were reduced. The population of FOC significantly decreased in the flooding soil incorporated with maize straw (20 g/kg soil) to 2.8% of untreated soil. Incorporation of lime decreased the population of FOC significantly as well, but less effectively than with maize straw did. ASD incorporated with maize straw (5 g/kg soil) could significantly decrease the disease incidence of banana, and a control efficiency of 69.5% was obtained in field experiment. These results indicated that ASD is an effective and environmentally friendly way to control banana Fusarium wilt disease.