The DNA of two Bacillus cereus strains, isolated from soy sauce residue, was extracted using a DNA extraction kit and purified using a gel recovery kit. A high-quality sequencing library was constructed, followed by whole-genome resequencing using Solexa sequencing technology. The quality of genome sequencing was assessed and the genomic information was analyzed. Mapping analysis was used to compare the mutant genes of two strains using the reference genome, the common mutant genes were singled out, and Clusters of Orthologous Groups (COG) annotation, Gene Ontology (GO) functional annotation, and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis were conducted on the common mutant genes. Using the results of these analyses of common mutant genes combined with previous literature related to salt tolerance of Bacillus cereus, the key genes that determine salt tolerance were singled out based on the analysis of gene function. In this study, 49 genes were found to be associated with salt tolerance that may play an important part in the process. The mechanism of salt tolerance was explored in this study, creating conditions for comprehensive utilization of soy sauce residue and providing an important basis for further research on the mechanism of salt tolerance in microorganisms during the fermentation of food.