[Background] Apple tree canker is widespread and dangerous. Currently, chemical control is the main way to prevent and cure it. However, there are some drawbacks. Therefore, it is urgent to find an effective and safe prevention and control measure. [Objective] In order to select Bacillus isolated in Saline-alkali soil from Dunhuang that showed significantly antagonistic effect on the Valsa mali growth. [Methods] The antifungal activities of selected Bacillus were investigated by dual culture assar and colony diameter assay, respectively. In addition, the control effect of antagonistic bacteria strains against Valsa mali in detached apple twigs in vitro and selection for medium were determined and the antagonistic Bacillus was identified based on morphological, physiological and biochemical characteristics and 16S rRNA gene phylogenetic analysis. [Results] The results revealed that strain 7-2-1-2 exhibited a strong antagonistic activity against V. mali, inhibiting significantly the germination of conidia and the growth of hyphae and especially the inhibitory rate of strain 7-2-1-2 was 86.18% and 73.2% in second screening. Strain 7-2-1-2 fermentation broth applied prior to wound inoculation of apple twigs with V. mali resulted in total inhibition of infection. The optimum growth medium of strain 7-2-1-2 was NBY. Strain 7-2-1-2 was identified as Bacillus subtilis subsp. spizizenii. [Conclusion] These results indicated that the strain 7-2-1-2 promised to provide a new biological control method in containing apple canker.