Objective: To evaluate the antiseptic effect of combined using of 5% sodium hypochlorite and calcium silicate-based root canal sealer against Enterococcus faecalis (Ef) biofilms in infected dentinal tubules in vitro. Methods: Cells of Ef were inoculated into the dentinal tubules of single-rooted teeth (without caries, periapical lesions and malformations extracted due to periodontal disease or orthodontic reasons; collected from Department of Maxillofacial Surgery, The First Affiliated Hospital of Zhengzhou University) with centrifugation and incubated in brain-heart infusion (BHI) to form 3-week-old biofilms. The infected samples were subjected to sodium hypochlorite or sterile water bathing for 10 minutes followed by calcium silicate-based root canal sealer (iRoot SP) (calcium silicate-based group), Gutta-percha group and sterile water group placed on the root canal wall for 1, 4 and 12 weeks. There were two samples in each treatment at each point. The antiseptic effectiveness of combined use of sodium hypochlorite and calcium silicate-based root canal sealer was analyzed by laser scanning confocal microscope (LSCM), ANOVA and LSD-t test. Results: After treatment with 5% sodium hypochlorite, in calcium silicate-based group for 4 and 12 weeks more Ef biofilm cells [(75.3±3.5)% and (74.8±3.8)%] were killed than in Gutta-percha group [(65.9±4.1)% and (63.0±3.7)%] and sterile water group [(63.9±4.0)% and (64.2±3.5)%] (P<0.05). After being treated with sterile water, the proportion of dead bacterial cells in calcium silicate-based group for 1, 4 and 12 weeks [(27.5±4.6)%, (43.0±4.4)% and (40.3±6.1)%] were more than those in Gutta-percha group and sterile water group (P<0.05). After being treated with 5% sodium hypochlorite or sterile water, more biofilm bacteria were killed in calcium silicate-based group for 4 and 12 weeks than in calcium silicate-based group for 1 week (P<0.05). Conclusions The combined use of sodium hypochlorite and calcium silicate-based root canal sealer kills more biofilm cells in infected dentinal tubules.