[Background] Bacillus is commonly used in microecological preparations next to lactic acid bacteria. However, some Bacillus spp. are not strictly regulated and pose potential safety hazards in application. [Objective] To study the prevalence of Bacillus cereus in Bacillus microecological preparations on sale from all over the country, and reveal the potential risks of the application of B. cereus. [Methods] B. cereus group strains were isolated and identified from the pretreated microecological preparations. Toxicity and antimicrobial resistance of B. cereus group strains were analyzed using whole-genome sequence. The cytotoxicity was evaluated via Cell Counting Kit-8 assay. Antimicrobial susceptibility was determined by broth microdilution methods. [Results] Twenty-three B. cereus group strains were isolated from 50 microecological preparations, which are resistant to ampicillin, lincomycin and tiamulin, and the detection rates of major virulence genes nhe, hbl, cytK, ces were 100%, 30%, 39% and 4%, respectively. All isolates were hemolytic and showed varying degrees of toxicity to Vero cell, 9 of which produced heat-stable toxins. [Conclusion] The widespread of toxin and resistance genes, and apparent observations of hemolytic activity, cytotoxic, and heat-stable toxin production in B. cereus group isolates from Bacillus microecological preparations, pose great threat to food safety and human safety. The findings highlights need for enhanced efforts required in the surveillance of risk factors, virulence factors and antimicrobial resistance in B. cereus from microecological preparations.