Staphylococcus aureus is one of the main pathogens involved in dairy cow mastitis. Monitoring antimicrobial resistance in S. aureus from raw milk is very important to make decisions regarding antibiotic treatments of animals from a food safety standpoint. The objective of this work was to investigate the prevalence of S. aureus strains isolated from different raw milk in China, and to characterize antimicrobial susceptibility of these strains and their key virulence genes. Raw milk samples of cow (n = 195), goat (n = 50), buffalo (n = 25), camel (n = 25), and yak (n = 25) were collected from 8 provinces in China. S. aureus was identified by biochemical identification and the nuc gene. Antimicrobial susceptibility patterns for recovered S. aureus isolates were determined by the agar disc diffusion method according to the guideline of the Clinical Laboratory Standard Institute. Antimicrobial resistance genes and virulence genes were tested by PCR. A total of 90 strains of S. aureus were isolated, included 54 strains from cow milks, 16 strains from goat milks, 9 from buffalo milks, 6 isolates from camel milks, and 5 isolates from yak milks. Among the 90 strains, antimicrobial resistance was most frequently observed topenicillin G (71.1%), followed by to ampicillin (61.1%), erythromycin (37.8%). The antimicrobial resistance S. aureus isolates were the most frequently observed in cow milk (79.6%), followed by goat milk (31.8%), camel (18%), buffalo (16.2%), and yak (7.69%). The most predominant resistance genes were blaZ (52.2%), mecA (24.4%), and cfxA (21.1%). The antimicrobial resistance genes were most frequently detected in S. aureus strains from cow milk (31.2%), followed by goat milk (26.9%), camel milk (14.1%), buffalo milk (10.24%) and yak milk (7.69%). The most predominant toxin genes were sec (22.2%), followed by sea (12.2%), and tst (12.2%). The majority of S. aureus strains were multidrug resistant and carried multiple virulence genes, which may pose a potential risk to public health. Our data indicated that the prevalence and antimicrobial resistance of S. aureus was a serious concern in different raw milks in China, which may pose potential risk to public health, especially cow milk and goat milk.