Inactivation mechanism of supercritical carbon dioxide (SC-CD) combination with Thymbra spicata essential oil (TEO) treatments on bacteria in tryptone soy broth (TSB) and juices was investigated. Salmonella Typhimurium was significantly inactivated by 3.45 and 5.55 logs after SC-CD+TEO treatment of TBS for 35 min at 7.6 and 10.13 MPa respectively. Klebsiella pneumoniae showed higher resistance to treatments than other two bacteria and Escherichia coli showed higher resistance to treatments than S. Typhimurium. Approximately 5.27, 4.68 and 3.82 logs inactivation of S. Typhimurium, E. coli and K. pneumoniae were obtained in the treatment of watermelon juice with SC-CD+TEO at 10.13 MPa after 35 min, while 6.89, 4.82 and 4.55 logs inactivated, respectively, were observed in melon juice. Research indicated that the inactivation mechanism involves inducing cell damage, increasing membrane permeability, increasing cell rupture, precipitation of cytoplasmic contents, extracting cellular substances and lysing cells. Different sensitivities of Gram-negative bacteria to the treatments may be attributed to the differences in the cell structure, compositions of membrane and presence of capsule, pressure level and exposure time. pH, total soluble solid and browning degree of juice did not significantly change after treatments and during 7 days of storage.