To analyze the effect of triple antibiotic paste on root canal microorganisms in periapical periodontitis of different stages.Eighty-nine children with periapical periodontitis of deciduous teeth in Department of Stomatology, Children's Hospital of Nanjing Medical University from April 2017 to April 2020 were enrolled, and divided into two groups according to the clinical symptoms and root X-ray films, i.e., acute inflammation group and chronic inflammation group. Samples of infected root canals were collected for bacterial identification, isolation and purification. The detection of microorganisms in the infected root canal and the composition of anaerobic microorganisms were analyzed in both groups. Disk diffusion method was used to observe antimicrobial effects of triple antibiotic paste and calcium hydroxide against common anaerobic bacteria, and the sensitivity of different anaerobic bacteria to triple antibiotic paste. Statistical analysis was completed by SPSS 20.0 software package.The microorganisms in both groups were mainly anaerobic bacteria. The detection rates of aerobes and anaerobic bacteria in the infected root canals had no significant difference between the two groups (P>0.05). The top five anaerobes detected in infected root canals were Peptostreptococcus, Bacteroidetes, Enterococcus faecalis, Porphyromonas gingivalis and Fusobacterium nucleatum. The detection rates of Porphyromonas gingivalis, Fusobacterium nucleatum and Bacteroidetes in infected root canal of acute inflammation group were significantly higher than those of chronic inflammation group, and the detection rate of Enterococcus faecalis was significantly lower than that of chronic inflammation group(P<0.05). The bacteriostatic circle diameter of triple antibiotic paste against Peptostreptococcus, Bacteroidetes, Enterococcus faecalis, Porphyromonas gingivalis and Fusobacterium nucleatum was significantly larger than that of calcium hydroxide(P<0.05). The sensitivity of different anaerobic bacteria to triple antibiotic paste was highest in Enterococcus faecalis, followed by Peptostreptococcus, Porphyromonas gingivalis, Fusobacterium nucleatum, and Bacteroidetes(P<0.05).Triple antibiotic paste has good antimicrobial effect on the common bacteria in the infected root canal of acute and chronic periapical periodontitis.