A suspected strain isolated from a batch of processed dairy products submitted by an import/export enterprise to our laboratory for the detection of Staphylococcus aureus was identified and analyzed. According to the Chinese national food safety standard Food Microbiological Examination: Staphylococcus aureus (GB 4789.10–2010), sampling and enrichment were performed, the suspected colony isolated on BP plates was subjected to hemolysis test on blood agar plates, microscopic observation after Gram staining, and plasma coagulase test before alignment, analysis and confirmation using a fully automated bacterial identification system and PCR. The suspected strain had a larger colony diameter compared with the reference strain of Staphylococcus aureus, showed white colonies on blood agar plates with no obvious hemolysis phenomenon but positive plasma coagulase test results, and was identified using a fully automated bacterial identification system and PCR as a nontypical strain of Staphylococcus aureus. In conclusion, real-time PCR enables rapid and accurate detection of Staphylococcus aureus while substantially shortening the detection time, and the possibility of missing the pathogen can be effectively overcome by combined use of different detection methods.