Carvacrol has great antibacterial activity against Bacillus cereus, and its action mechanism was comprehensively studied in this work. It could not only control the growth of B. cereus by affecting the integrality of cellular structure and physiological metabolism, but also inhibit the swarming motility, biofilm formation, and toxins production. To increase the stability of carvacrol during the application, the sodium casein (SC)/hydroxypropyl-β-cyclodextrin (HPCD)/carvacrol nanoemulsion was fabricated. The mean particle size and polydispersity index of the nanoemulsions were 113.8 nm and 0.23, respectively, at SC and HPCD concentrations of 2% and 1%. FTIR analysis demonstrated that carvacrol was successfully encapsulated into the nanoemulsions. The MIC and MBC of nanoemulsions against B. cereus were 0.15 and 0.30 mg/mL, respectively, which were lower than those of free carvacrol (0.19 and 0.38 mg/mL). Carvacrol in nanoemulsions showed a slow and sustained release behavior. Furthermore, the nanoemulsions had good stability (particle size <200 nm) after storage at 4 °C and 25 °C for 15 days. Notably, the nanoemulsions were effective in controlling the growth of B. cereus in whole, low-fat, and skim milk and had better antimicrobial activity than free carvacrol. The results indicated that carvacrol nanoemulsions have potential in the antibacterial application of the food industry.