The invention discloses a method for preparing cheese containing prebiotics bacillus amyloliquefaciens. The method for preparing the cheese comprises the following steps: pretreating raw milk, performing inoculating fermentation, preparing a bacteria-containing enzyme solution, performing rennet coagulation, cutting, discharging whey, stacking for fermenting, squeezing for forming, packaging and maturing. According to the cheese disclosed by the invention, the varieties of probiotics are rich, the cheese contains bacillus amyloliquefaciens with the probiotics function in addition to lactic acid bacteria, the intestinal probiotics group can be effectively improved, and digestion and absorption are promoted. According to the method, direct rennet coagulation is performed by adopting fermentation liquor of bacillus amyloliquefaciens, centrifuging and other operations are not needed, and thus the production cost can be saved. According to the cheese produced by the method, the varieties of cheese can be enriched, and more choices are provided for consumers.