Objective To explore the characteristics of antimicrobial resistance, virulence factor and sequence typing of food-borne Staphylococcus aureus in China. Methods The antimicrobial susceptibility testing of S. aureus was carried out following broth microdilution method. Meanwhile, multilocus sequence typing (MLST), the important antibiotic resistance gene mecA, and virulence genes were analyzed based on whole genome sequencing.. Results The overall resistance rate of the 224 foodborne S. aureus isolates to 12 classes of antibiotics was 87.9%, with the highest resistance rate of 82.6% to penicillin. The multi-drug resistance rate was 23.2%, with ST398 accounting for the highest percentage of multi-drug resistant bacteria. The prevalence rate of MRSA was 8.0%, and the ST types of MRSA mainly included ST1, ST59, ST398, ST6, ST9, ST45, and ST72. The overall carriage rate of staphylococcal enterotoxin genes was 52.2%, among which sea had the highest carriage rate of 24.6%. The ST type carrying the most types of enterotoxin genes was ST1. A total of 31 ST types were detected in this study, among which ST7 were the predominant ST of isolates, followed by ST398. In addition, the carriage rates of toxic shock syndrome toxin coding gene (tsst-1) and leukocytocin encoding genes (lukF-PV and lukS-PV) were 6.3% and 4.5%, respectively. Conclusion The high rate of antimicrobial resistance and enterotoxin genes carriage of food-borne S. aureus in China, and the detection of virulence genes that play an important role in clinical infection suggest that the potential hazards of S. aureus in food should not be ignored. There is a high correlation between ST type and food type, antimicrobial susceptibility and pathogenicity, which provides scientific data for further analysis of the epidemiological characteristics and risk prevention and control of foodborne S. aureus in China.