Green huajiao (Zanthoxylum schinifolium) essential oil (GHJEO) is a natural medicinal and flavoring essential oil. GHJEO has been reported to show good antibacterial activity as a promising alternative to chemical food preservatives in the food industry. However, the antibacterial mechanism of GHJEO has rarely been reported. In this study, we analyzed the antibacterial mechanism of GHJEO against Bacillus cereus at the physicochemical, morphological and metabolic levels. GHJEO contained many previously reported antibacterial components. The MIC and MBC of GHJEO against B. cereus were determined to be 2.0 and 4.0 mg/mL, respectively. We found that GHJEO could destroy the cell wall and membrane of Bacillus cereus, causing cytoplasmic leakage. In addition, GHJEO at a subinhibitory concentration (0.5 MIC) could cause significant metabolic changes of B. cereus. Further bioinformatics analysis revealed that GHJEO could cause cell membrane damage, energy metabolism disorders, and amino acid metabolism disorders. The results of this study may be beneficial for the development and application of GHJEO in food safety.