Objective To compare the antibacterial effect and short-term clinical effect of new triple antibiotic paste (ornidazole, ciprofloxacin and minocycline) used alone and in combination with calcium hydroxide paste against Enterococcus faecalis in root canal retreatment. Methods A total of 149 single rooted teeth with failed endodontic treatment were selected in the present study. The samples were randomly divided into 5 groups:calcium hydroxide paste group (CH group), triple antibiotic paste (metronidazole, ciprofloxacin and minocycline) group (TAP group), new triple antibiotic paste group (NTAP group), the combination group of calcium hydroxide paste and new triple antibiotic paste (CH+NTAP group), and camphor phenol group (CP group). After removal of the root-filling material, the quantities of Enterococcus faecalis in the root canals were determined before and after root canal preparation and 7 d after root dressing. The short-term clinical effects were evaluated 7 d after root dressing in each group. Results After root canal preparation and root dressing of 7 d, the quantities of Enterococcus faecalis in root canals in each group were significantly decreased versus before root canal preparation (all P<0.05). After 7 d root dressing, the quantities of Enterococcus faecalis of each group were significantly lower versus after root canal preparation (all P<0.05). The quantities of Enterococcus faecalis were significantly lower in the CH, TAP, NTAP and CH+NTAP groups than that in the CP group (all P<0.05), those in the NTAP group and CH+NTAP group were significantly lower than those in the CH group and TAP group (all P<0.05), and that in the TAP group was significantly lower than that in the CH group (P<0.05). After 7 d root dressing, the CH, TAP, NTAP and CH+NTAP groups had better clinical effects than the CP group (all P<0.05), and the clinical effects of the TAP group, NTAP group and CH+NTAP group were better than that of the CH group (all P<0.05), while there was no significant difference between the TAP group, NTAP group and CH+NTAP group (P>0.05). Conclusion Calcium hydroxide paste and triple antibiotic paste alone or in combination have better antibacterial effect for root canal disinfection against Enterococcus faecalis in root canal retreatment. They also have better short-term clinical effect, especially the new triple antibiotic paste, which can be considered as an effective alternative intracanal medicament and is worthy of clinical application.