The key of the root canal therapy is to eliminate the micro-organism infection, fill the root canal tightly and reduce the stimulation to the periapical tissues. However, it is quite difficult to meet all the conditions due to the defect of the material. Here we develop a novel root canal sealer (MZOE), in which zinc oxide eugenol (ZOE) were fabricated with polyhexamethylene guanidine (PHMG), and the PHMG’s concentration is 0.8, 1.0, 1.2 and 1.4%. Our investigation tested its physical properties, antibacterial effect to E. faecalis, C. albicans, E. coli, S. aureus and cytotoxicity to human periodontal ligament fibroblasts (HPDLFs). The physical properties of the MZOE conformed to the ISO 6876:2001, and its antibacterial effect was stronger than ZOE (p<0.05), the RGR of HPDLFs was tested between 1 to 24%, belonging to moderate cytotoxicity. It was suggested that MZOE had good physical properties, high antibacterial effect, and moderate cytotoxicity.