Background and Aims Intersphincteric resection (ISR) has been proven to achieve good oncological outcomes as an ultimate sphincter-preserving surgery for ultra-low rectal cancer. Due to its maximal preservation of the anus and avoidance of permanent stoma, ISR has gradually become an important option for sphincter-preserving surgery for low rectal cancer. However, ISR involves partial or complete resection of the internal anal sphincter, inevitably leading to a decrease in postoperative anal function. Anastomotic leakage is one of the most common complications after ISR and may have an adverse effect on postoperative anal function. However, there is no thorough study on the specific effect of anastomotic leakage on anal function in patients after ISR. Therefore, this study was performed to investigate the impact of anastomotic leakage on short- and long-term anal function in patients after ISR.Methods The clinical and follow-up data of 236 patients undergoing ISR with a diverting loop ileostomy from June 2011 to January 2022 in the PLA Rocket Force Characteristic Medical Center were retrospectively collected. The general clinical data between patients who developed anastomotic leakage and those who did not were compared. Differences in the Wexner incontinence score (WIS) and low anterior resection syndrome (LARS) score, as well as differences in various parameters of anorectal manometry at 6 months and 2 years after ileostomy reversal, were compared between patients with and without anastomotic leakage.Results Among the 236 patients, 41 cases (17.4%) developed anastomotic leakage, and 23 (9.7%) ultimately did not undergo ileostomy reversal. Comparison of general clinical data between patients with and without anastomotic leakage showed that patients with anastomotic fistula had a higher BMI (27 kg/m² vs. 25 kg/m²), a higher incidence of diabetes (29.3% vs. 15.9%), longer operative time (222 min vs. 200 min), and a significantly higher proportion of ileostomy non-reversal (34.1% vs. 4.6%), all of which were statistically significant (all P<0.05). A total of 149 patients completed anal function questionnaires at 6 months and 2 years after ileostomy reversal, of whom 20 (13.4%) had anastomotic leakage and 129 (86.6%) did not. At 6 months after closure, the WIS score (12 vs. 9) and LARS score (34 vs. 29) of patients with anastomotic leakage were higher than those without (both P<0.05); however, at 2 years after closure, there were no statistically significant differences in WIS score (8.5 vs. 8) and LARS score (28.5 vs. 32) between the two groups of patients (both P>0.05). A total of 53 patients completed rectal manometry examinations at 6 months and 2 years after ileostomy closure, of whom 11 (20.8%) had anastomotic leakage and 42 (79.2%) did not. At 6 months after closure, the maximum squeeze pressure of the anal canal in patients with anastomotic leakage was higher than that in patients without (P<0.05), while other parameters including resting pressure of the anal canal, length of the high-pressure zone of the anal canal, and maximum tolerable volume showed no statistical differences between the two groups of patients (all P>0.05); at 2 years after closure, there were no statistical differences in all parameters of anorectal manometry between the two groups of patients (all P>0.05).Conclusion The occurrence of anastomotic leakage increases the risk of permanent stoma after ISR. For patients who have restored intestinal continuity, anastomotic leakage has a negative impact on early anal function, but may not have a significant impact on long-term anal function.