Objective To establish a new quantitative accuracy method for detection of Staphylococcus aureus in food by droplet digital polymerase chain reaction PCR polymerase chain reaction (ddPCR). Methods A pair of primers and probe for both qPCR and ddPCR was selected according to the single copy gene of nuc in Staphylococcus aureus. The specificity, sensitivity, accuracy and repeatability of this method were analyzed. Results The limit of detection (LOD) and limit of quantitation (LOQ) of ddPCR method were determined to be 110 CFU/mL by gradient dilution of pure culture of Staphylococcus aureus. The LOQ of ddPCR was 1 000 CFU/g in the artificial contaminated experiment, and the maximum deviation of detection result of four spiked addition levels was 4.77%, and the coefficient of variation of 5 parallel repeats was less than 20%, showing good accuracy and repeatability. Conclusion The established method has good specificity, high sensitivity and accurate result, which provides a reference for rapid quantitative detection of Staphylococcus aureus.