The invention discloses Bacillus atrophaeus and an application thereof. The Bacillus atrophaeus JZB120050CGMCC No.10919 has stable, efficient and broad-spectrum antibacterial properties. The Bacillus atrophaeus can generate a biological membrane, has strong capability of generating siderophore, chitinase, cellulase and protease, which shows that the strain has relatively strong biocontrol potential. The control effect of fermentation liquor of the strain to tomatoes inoculated with botrytis cinerea for culturing 11d is 100% (the control effect of a 5-time diluent treatment group of JZB120050 strain fermentation liquor is 48%, the control effect of a treatment group of JZB120028 strain fermentation liquor is 50%, the control effect of a 5-time diluent treatment group of JZB120028 strain fermentation liquor is 26%, and the control effects of a blank control group, a 1000-time liquid treatment group of 3% polyoxin, and 1000-time liquid treatment group of 50% carbendazim are 0%), which shows that the strain has an effective inhibitory action on the botrytis cinerea. The strain is safe to human and domestic animals, does not have environmental pollution problems, is simple in culture condition, easy to store and suitable for industrial production, and has a good development application prospect.