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Handmade dairy products, which retain the nutrients in milk to the greatest extent, have become popular in China recently. However, no investigation regarding the characteristics of <i>Staphylococcus aureus</i> (<i>S. aureus</i>) in raw milk of handmade dairy retail stores has been reported. Here, we investigated the antimicrobial susceptibility, virulence, biofilm formation, and genetic diversity of <i>S. aureus</i> in raw milk from handmade dairy retail stores in Hefei, China. After 10 months of long-term monitoring, 50 <i>S. aureus</i> strains were isolated from 69 different raw milk samples, of which 6 were positive for methicillin-resistant <i>S. aureus</i> (MRSA). The resistance rates of these isolates to ampicillin, erythromycin, kanamycin, tetracycline, sulfamethoxazole-trimethoprim, gentamicin, ofloxacin, oxacillin, chloramphenicol, and doxycycline were 56, 54, 40, 24, 22, 22, 18, 14, 8 and 6%, respectively. All 50 isolates were susceptible to vancomycin and 29 strains (58%) showed multidrug resistance phenotype. For enterotoxins genes, <i>selp</i> (14%) was detected the most frequently, followed by <i>sea</i> (6%), <i>sec</i> (4%), <i>sei</i> (4%), <i>ser</i> (4%), <i>selj</i> (4%), and <i>seh</i> (2%). By microplate assay, 32 and 68% of the strains showed moderate and strong biofilm formation ability, respectively. Fifty isolates were discriminated into nine <i>spa</i> types, and the most common <i>spa</i> typing was t034 (42%). The results of this study indicate that <i>S. aureus</i> from raw milk may constitute a risk concerning food poisoning, and more attention must be given to awareness and hygienic measures in the food industry.