The aim of this study is to investigate the genetic backgrounds of methicillin susceptible Staphylococcus aureus (MSSA), methicillin-resistant Staphylococcus aureus (MRSA) and heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) isolates isolated from clinical specimens of the patients with verified infections in a Chinese teaching hospital. Macro E test (MET) was used to detect hVISA and multilocus sequence typing (MLST) was used to determine the STs of the selected isolates. The genotypes of SCCmec were determined by multiplex polymerase chain reaction (PCR) in MRSA isolates. Panton-valentine leucocidin (PVL) genes were also detected by PCR. Among 273 S. aureus isolates, hospital-acquired methicillin-resistant Staphylococcus aureus (HA-MRSA), community-associated methicillin-resistant S. aureus (CA-MRSA), hospital-acquired methicillin susceptible Staphylococcus aureus (HA-MSSA) and community-associated methicillin susceptible Staphylococcus aureus (CA-MSSA) isolates accounted for 55.6, 1.5, 36.3, and 6.6%, respectively. Nine isolates were confirmed as hVISA by MET. Among 60 HA-MRSA isolates, ST239-MRSA-III was the most prevalent clone accounting for 51.7%, followed by ST5-MRSA-II clone. Fifty percentage and 22.2% of CA-MSSA isolates were found to be ST121 and ST88. ST239-MRSA-III was the predominant clone in hVISA isolates. However, no predominant ST type was found in HA-MSSA isolates. Of 9 PVL-positive strains, ST88 was the most prevalent ST (50.0%; 4/8), followed by ST121 (33.3%; 3/9), ST5 (4.5%; 1/22) and ST239 (2.6%; 1/39). In conclusion, ST239-III was the major pandemic clone in hVISA and HA-MRSA and spread in China. ST5-emerging rapidly in China had remained stable viability.