The aim of this study was to investigate the molecular characteristics of community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) isolates from Chinese children. Ninety-nine isolates were collected from eight hospitals, and analyzed by multilocus sequence typing, staphylococcal chromosomal cassette mec (SCCmec) type, and spa typing. The Panton-Valentine leukocidin (PVL) gene was also detected. Overall, 14 sequence types (STs) were obtained, and ST59 (58.6%) was found to be the most prevalent, followed by ST1 (8%) and ST338 (8%). We also first registered the new ST1409. SCCmec type IV was the most predominant type at 67.7%, followed by SCCmec type V at 32.3%. SCCmec subtypes IVa, IVc, and IVg were found among the SCCmec type IV strains. Twenty-one spa types were also identified. Four new spa types were found by synchronization with the Ridom SpaServer and referring to the website (http://www.SeqNet.org). ST59-MRSA-IVa with t437 accounted for 40.4% of occurrences, making it the most prevalent clone. The prevalence of PVL genes was 58.6%, and multidrug resistance was observed in 95% of all isolates. This result indicates that CA-MRSA isolates in Chinese children are largely associated with the ST59-MRSA-IV clone, and that the predominant clones of CA-MRSA are spread all over the country.