Abstract: Objective: To investigate the underlying mechanism of cinnamon essential oil nanoemulsion (CON)-induced inactivation of Pseudomonas deceptionensis CM2 with the non-targeted metabolomics approaches. Methods: P. deceptionensis CM2 was treated with CON for 4 h, and the differential metabolites were identified by liquid chromatography-mass spectrometry combined. The number and type of differential compounds and their regulatory expression in metabolic pathways were also analyzed. Results: The minimum inhibitory concentration (MIC) of CON against P. deceptionensis CM2 was 0.125 μL/mL. Multivariate statistical analysis showed that there were significant differences in the metabolic profiles of P. deceptionensis CM2 after exposure to CON at 1×MIC for 4 h. For P. deceptionensis CM2 cells treated with CON at 1×MIC for 4 h, a total of 380 differential metabolites were identified, mainly including heterocyclic compounds, aromatic compounds, lipids, organic acids, etc. Among these differential metabolites, 309 metabolites were significantly up-regulated (P<0.05), and 71 metabolites were significantly down-regulated (P<0.05). These differential metabolites were mapped onto 13 metabolic pathways, mainly including the metabolism of amino acids, purine, amino sugar, pyrimidine, etc. Conclusion: CON might inactivate P. deceptionensis CM2 by affecting some metabolic pathways, such as amino acids biosynthesis and energy metabolism. This study would provide a theoretical basis for the application of CON in food preservation.