Staphylococcus aureus or methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of surgical site infections (SSIs). The aim of our study was to characterize molecularly S. aureus isolates from SSIs in orthopedic patients in Shanghai, China. Eighty-two S. aureus isolates (46 methicillin-susceptible Staphylococcus aureus [MSSA] and 36 MRSA) were collected from SSIs in orthopedic patients. Antimicrobial susceptibility testing was performed according to the Clinical and Laboratory Standards Institute (CLSI) guidelines and a variety of clinically important toxin genes were detected. The sequence type, spa type, and agr group were determined to analyze the genotypes of all the isolates collected. In addition, MRSA isolates were characterized by staphylococcal cassette chromosome mec (SCCmec) type as well. The strains showed susceptibility to antibiotics such as teicoplanin, minocycline, quinupristin-dalfopristin, linezolid, mupirocin, and vancomycin. Ten pvl-positive isolates (three MRSA and seven MSSA) were found among all isolates. Eight community-associated MRSA (CA-MRSA) isolates were found, six of which belonged to ST59-MRSA-IV but most MRSA isolates (20/36, 55.6%) belonged to ST239-MRSA-III-t030/t037 with a wide range of antibiotic resistance. By contrast, MSSA isolates were more diverse in both molecular characterizations and virulence factors, with eight MSSA isolates harboring more than six toxin genes detected. ST239-MRSA-III-t030/t037 was the epidemic clone, and healthcare-associated MRSA (HA-MRSA) strains might be the major pathogen causing S. aureus SSIs in orthopedic patients.