Staphylococcus aureus (S. aureus) is known to be one of the most common foodborne pathogens capable of secreting a wide range of exotoxins such as enterotoxin, which severely threatens the health of consumers. Over the past few years, the development of safe and effective strategies in inhibiting the growth and enterotoxins generation of S. aureus in food turns out to be the research focus and emphasis. This research explores citronellal (CIT), a native compound with extensive existence in spices, which could effectively inhibit the growth and enterotoxins generation of S. aureus (ATCC 29213). Results from minimal inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and time-kill curves, showed that CIT could tremendously inhibit the growth of S. aureus. Analysis on hemolysin showed that CIT at sub-MIC could significantly (p < 0.05) inhibit the hemolytic activity of S. aureus. As revealed by the results of ELISA, the production of enterotoxins in the culture supernatant and pork meat decreased significantly (p < 0.05) after exposure to CIT at sub-MIC. Furthermore, a significant (p < 0.05) decrease in dose-dependent was found in the transcription levels of virulence-related genes. In all, CIT proved to be a possible inhibitor of the growth and enterotoxins production of S. aureus with highly promising application in the food industry.