Objective To compare the safety and efficacy between endoscopic incision (EI) and endoscopic balloon dilation (EBD) for treating refractory anastomotic stricture after surgery of sigmoid colon and rectum. Methods Clinical data of the 24 patients with refractory benign anastomotic stricture after surgery of sigmoid colon and rectum who received EI or EBD at the second Xiangya hospital from June 2009 to September 2015 were retrospectively analyzed. They were divided into group EI and group EBD. Safety and efficacy between the two groups were compared based on preoperative, intraoperative, and 1, 6, 12, 24 months postoperative data. Results There were 12 patients in each group, and all patients received EI or EBD treatment successfully with the success rate of 100%. No patient developed serious complications such as obvious bleeding, perforation during or after treatment. All strictures were successfully managed and the obstruction symptoms were relieved. As for the short-term efficacy, the symptom relief rate and endoscopic patency rate of EI and EBD 1 and 6 months after a single treatment were comparable (P>0.05). As for the medium to long-term efficacy, the symptom relief rate and endoscopic patency rate of EI 12 and 24 months after a single treatment was higher than that of EBD (P<0.05). The mean follow-up of EI and EBD group was 24.4 months and 28.5 months, and the median treatment sessions in each group was 1.0 and 2.5 respectively, the total treatment session in the EI group was less than that in the EBD group(1/12 VS 9/12), and the anastomotic diameter of EI group at final check was larger than that of EBD group (1.833±0.293 cm VS 1.608±0.183 cm, P<0.05). Conclusion EI could result in a better medium-to-long-term efficacy than EBD and reduce the rate of recurrence. Key words: Constriction, pathologic; Surgical stomas; Sphincterotomy, endoscopic; Balloon dilation; Comparative effectiveness research