Pathogen detection was carried out in two food poisoning incidents in Nanan District, Chongqing City, to provide a basis for disposal and determination of such incidents. Pathogens were isolated and identified from anal swabs of cases and practitioners, samples of the food processing environment and retained food. The isolates were subjected to enterotoxin detection and drug sensitivity tests, and whole genome sequencing was performed to obtain virulence and resistance genes carried by the isolates, as well as multilocus sequence typing and single nucleotide polymorphism analysis. Ten strains of S. aureus were isolated from anal swabs of eight cases, one environmental sample, and one retained food sample, of which four and six strains were isolated from two incidents, respectively. In the same incident, S. aureus produced the same enterotoxin with the same resistance profile.Pathogens producing enterotoxin SEA, SEE both carried the virulence gene sea and Pathogens producing enterotoxin SEA, SEB, SEE both carried the virulence genes sea and seb. the resistance profiles were PEN-ERY and PEN respectively. The isolates with resistance profiles PEN-ERY , all carried the associated resistance genes blaZ and erm(A) except for one isolate that did not carry the associated resistance gene blaZ, whereas the isolates with resistance profiles PEN all carried the associated resistance gene blaZ. MLST analysis showed 100% homozygosity for the same event, ST30 type , ST59 type respectively. Single nucleotide polymorphism analysis of the same event was highly homologous. Therefore, these two events were both food poisoning events caused by S. aureus contamination, which were resistant to penicillin. Based on whole genome sequencing, multi-locus sequence typing and single nucleotide polymorphism analysis of the strains can be used for homology analysis of aggregation events caused by S. aureus.