To evaluate the potential application value of metagenome sequencing in foodborne disease outbreak. Method Four suspect food samples from a foodborne disease outbreak caused by Staphylococcus aureus were sequenced by metagenome sequencing, ?structures of microbial communities, foodborne pathogen and toxic genes were analyzed based on the sequencing data. Result The result of metagenome sequencing showed that structures of microbial communities were complex. The relative abundance of 18 foodborne pathogens was low. However, the relative abundance of S. aureus among 18 foodborne pathogens was high. The toxic genes of S. aureus were not detected. Conclusion It is difficult to confirm the pathogen causing disease for complex microbial communities in food samples. However, metagenome sequencing needs no prediction of potential pathogens in samples, which is more conducive to detect mixed pathogens causing foodborne disease. Therefore, metagenome sequencing would be helpful method in investigating foodborne disease outbreak under the sufficient sequencing depth.