Abstract: Bacillus cereus enhances its environmental tolerance through biofilm formation and spore production. This strong environmental tolerance is a significant factor of recurrent contamination in dairy products by Bacillus cereus. With the aim of further exploring the tolerance of Bacillus cereus and effectively controlling it in actual production, this study cultured the conditionally screened Bacillus cereus in five different media types (TSB, LB, NB, whole milk, and skim milk). On this basis, its tolerance under acid-base, osmotic pressure, disinfectant, and high-temperature stress conditions was examined. The relevant tolerance genes were analyzed by means of whole-genome sequencing technology, and the morphological changes under environmental stress were observed and analyzed through microscopic structure. In this research, 55 strains of Bacillus cereus isolated from the processing environment of infant formula milk powder were taken as the research objects. Through a comprehensive assessment of biofilm formation and spore generation capabilities, the representative BC2 strain was selected as the test strain. The research findings revealed that there were 20 genes related to biofilm and 43 genes related to spore formation in BC2, respectively, and there were also numerous environment-tolerance-related genes. Moreover, the results indicated that the BC2 strain possessed a strong environmental adaptability and demonstrated robust stress resistance in the TSB medium. By using field emission scanning electron microscopy for observation, it was discovered that the morphology of BC2 cells underwent different changes under different environmental stresses, further manifesting its strong tolerance at the microscopic structure level.