Objective: To construct a model of Enterococcus faecalis (E. faecalis) infection in dentinal tubules by gradient centrifugation and to evaluate the antibacterial effect of low-temperature plasma on E. faecalis in dentinal tubules. Methods: Standard dentin blocks of 4 mm×4 mm×2 mm size were prepared from single root canal isolated teeth without caries, placed in the E. faecalis bacterial solution, centrifuged in gradient and incubated for 24 h to establish the model of dentinal tubule infection with E. faecalis. The twenty dentin blocks of were divided into five groups, low-temperature plasma jet treatment for 0, 5 and 10 min, calcium hydroxide paste sealing for 7 d and 2% chlorhexidine gel sealing for 7 d. Scanning electron microscopy and confocal laser scanning microscope were used to assess the infection in the dentinal tubules and the antibacterial effect of low-temperature plasma. Results: The results of scanning electron microscopy and confocal laser scanning microscopy showed that after 24 h of incubation by gradient centrifugation, E. faecalis could fully enter the dentinal tubules to a depth of more than 600μm indicating that this method was time-saving and efficient and could successfully construct a model of E. faecalis infection in dentinal tubules. Low-temperature plasma could enter the dentinal tubules and play a role, the structure of E. faecalis was still intact after 5 min of low-temperature plasma treatment, with no obvious damage, and after 10 min of low-temperature plasma treatment, the surface morphology of E. faecalis was crumpled and deformed, the cell wall was seriously collapsed, and the normal physiological morphology was damaged indicating that the majority of E. faecalis was killed in the dentinal tubules. The antibacterial effect of low-temperature plasma treatment for 10 min exceeded that of the calcium hydroxide paste sealing for 7 d and the 2% chlorhexidine gel sealing for 7 d. These two chemicals had difficulty entering deep into the dentinal tubules, and therefore only had a few of antibacterial effect on the bacterial biofilm on the root canal wall, and there was also no significant damage to the E. faecalis bacterial structure. Conclusion: Gradient centrifugation could establish the model of E. faecalis dentin infection successfully. Low-temperature plasma treatment for 10 min could kill E. faecalis in dentinal tubules effectively, which is superior to the calcium hydroxide paste sealing for 7 d and the 2% chlorhexidine gel sealing for 7 d.