We isolated strains from the rhizosphere soil of apple trees with replanting disease and evaluated the biological control potential for the pathogens Fusarium proliferatum, F. moniliforme, F. oxysporum, and F. solani. The morphological, physiological and biochemical character, and 16S rDNA sequence of the strain with the highest inhibitory rate were analyzed. The effect of strain biofertilizer on the biomass of Malus hupehensis Rehd. seedlings and soil environment under replanting disease was evaluated in a pot experiment. The results showed that the strain B6 had the strongest antagonistic activity. The inhibitory rate of B6 for F. proliferatum, F. moniliforme, F. oxysporum, Fusarium solani reached 71.8%, 70.1%, 72.6% and 91.5%, respectively. The strain B6 was identified as Bacillus methylotrophicus according to the results of morphological, physiological and biochemical character and 16S rDNA sequence analysis. Compared with the control, the bacterial manure made from the strain B6 enhanced the biomass of Malus hupehensis Rehd. seedlings in replanting soil to different extent. The ground diameter, fresh and dry mass were significantly increased by 18.3%, 49.6% and 51.2%, respectively. The strain B6 dramatically increased the number of cultivable bacteria and actinomyces in replanting soil and reduced the abundance of fungus to 37.7%, which accelerated the conversion of fungal soil to bacterial soil. It also dramatically increased the activities of sucrase, phosphatase, ureaseandcatalase in soil by 37.3%, 24.0%, 42.9% and 49.4%, respectively. In conclusion, the B6 fertilizer could improve the structure of cultivable microbial communities in the continuous cropping soil of apple trees, increase the soil enzyme activity, and enhance the growth of Malus hupehensis seedlings.