Background: Mesoporous calcium-silicate nanoparticles (MCSNs) have good prospects in the medical field due to their great physicochemical characteristics, antibacterial activity and drug delivery capacity. This study was to analyze the antibiofilm activity and mechanisms of silver (Ag) and zinc (Zn) incorporated MCSNs (Ag/Zn-MCSNs) with different percentages of Ag and Zn. Methods: Ag/Zn(1:9, molar ratio)-MCSNs and Ag/Zn(9:1, molar ratio)-MCSNs were prepared and characterized. Endocytosis of nanoparticles by Enterococcus faecalis (E. faecalis) treated with Ag/Zn-MCSNs was observed using TEM to explore the antibacterial mechanisms. The antibiofilm activity of Ag/Zn-MCSNs with different ratios of Ag and Zn was tested by E. faecalis biofilm model in human roots. The human roots pretreated by different Ag/Zn-MCSNs were cultured with E. faecalis. Then, SEM and CLSM were used to observe the survival of E. faecalis on the root canal wall. Cytotoxicity of the nanoparticles was tested by CCK8 kits. Results: The Ag/Zn-MCSNs release Ag + and destroy the cell membranes to kill bacteria. The MCSNs containing Ag showed antibacterial activity against E. faecalis biofilms in different degrees, and they can adhere to dentin surfaces to get a continuous antibacterial effect. However, MTA, MCSNs and Zn-MCSNs could not disrupt the bacterial biofilms obviously. MCSNs, Ag/Zn(1:1, molar ratio)-MCSNs and Ag/Zn(1:9)-MCSNs showed no obvious cytotoxicity, while Ag-MCSNs and Ag/Zn(9:1)-MCSNs showed cytotoxicity. Zn-MCSNs can slightly promote cell proliferation. Conclusion: Ag/Zn-MCSNs have good antibiofilm activity. They might achieve an appropriate balance between the antibacterial activity and cytotoxicity by adjusting the ratio of Ag and Zn. Ag/Zn-MCSNs are expected to be a new type of root canal disinfectant or sealer for root canal treatment.