Objective To investigate the contamination and characterization of Staphylococcus aureus in meats of animal origin in Huai'an. Methods 378 meat samples of animal origin were collected from 8 counties in Huai'an during 2017 to 2018 and were tested for S.aureus. The agar diffusion method was used in antimicrobial susceptibility test and polymerase chain reaction (PCR) was used to detect the S.aureus enterotoxin genes. Results Of the total 378 samples, 60 samples (15.87%) were positive for S.aureus. And the positive rate of duck, chicken, beef, pork and mutton were 22.50% (18/80), 17.95% (14/78), 15.38% (10/65), 12.94% (11/85) and 10.00% (7/70), respectively. The antimicrobial susceptibility test indicated that S.aureus isolates showed the highest resistance to clindamycin (71.67%,43/60) and were all sensitive to vancomycin. Multidrug resistant strains accounted for 63.33% (38/60) and the methicillin resistant S.aureus strains accounted for 23.33% (14/60). The carriage rate of enterotoxin gene sea, seb, sec, sed and see were 6.67%(4/60), 6.67%(4/60), 23.33%(14/60), 48.33%(29/60)and 10.00%(6/60), respectively. And the carriers of toxic shock syndrome toxin-1 gene tsst-1 was 5.00%(3/60). The detection rates of drug resistance gene ant(4′,4″), mecA, vanA and tetM were 88.33%(53/60), 13.33%(8/60), 11.67%(7/60) and 8.33%(5/60), respectively. Conclusion The contamination of S.aureus in meats of animal origin in Huai'an was serious, and the isolates showed high antibiotic resistance and high carriage rate of enterotoxin genes, which may result in potential risks to food safety.