Tobacco planting soil with severe continuous cropping obstacles were treated by physical fumigation, chemical fumigation and reductive soil disinfestation based on sugarcane bagasse, with untreated soil as the control. Then, the changes in the soil physicochemical properties and microbial communities were analyzed, and FUNGuild platform was applied for functional prediction of fungal communities. Results showed that compared with the control, chemical fumigation significantly increased the content of hydrolyzed nitrogen in the soil, physical fumigation significantly increased the content of available phosphorus and available potassium, and reductive soil disinfestation significantly increased the pH value and organic matter content of the soil. The number of Fusarium oxysporum in the soil treated with physical fumigation, chemical fumigation, and reductive soil disinfestation decreased by 26.74%, 41.39% and 38.46%, respectively; these sterilization methods all had inhibitory effects on Fusarium oxysporum in tobacco planting fields. The composition of microbial communities in soil changed significantly with different disinfestation methods. Chemical fumigation and reductive soil disinfestation increased the relative abundance of Bacillus, Tuberibacillus, Clostridium, and Bacteroides in the soil. In reductive soil disinfestation treated soil, Hydrogenospora, Ruminiclostridium and Bacteroides are the dominant bacterial genera. Function prediction for microbial community shows that physical fumigation leads to an increase in pathotrophic fungi in the soil, chemical fumigation transforms nutritional type of fungi from saprotroph-symbiotroph to pathotroph-symbiotroph, and reductive soil disinfestation significantly reduces the abundance of pathotrophic fungi and promotes the large-scale reproduction of saprophytic fungi.