Background <p>To evaluate the clinical efficacy and safety of intersphincteric incision and fistula ligation in the treatment of transphincteric anal fistula.</p> Methods <p>This retrospective study analyzed the clinical data of 84 patients with transphincteric anal fistula who underwent intersphincteric incision and fistula ligation at the National Center for Colorectal Disease Treatment, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine from January 2024 to October 2024. Cure rates, pre- and postoperative Wexner anal incontinence scores, and postoperative complications were recorded.</p> Results <p>Among the 84 patients, 77 [91.67%, 95% confidence interval (CI) = 84.63–96.77) were cured after a single surgery. The pre- and postoperative Wexner anal incontinence scores of all patients were unchanged (<i>P</i> = 0.483). Of the 84 patients, six patients (7.1%, 95% CI = 2.7–14.9) experienced postoperative urinary retention, with no cases of postoperative bleeding or incision infection. No patients who only underwent intersphincteric incision and fistula ligation exhibited postoperative “lock-eye” deformity of the anus. Postoperative pain was uniformly mild, and full satisfaction with outcomes was reported.</p> Conclusions <p>The combination of intersphincteric incision and fistula ligation for transphincteric anal fistula offers high cure rates, good anal function protection, and low postoperative complication rates, reflecting a safe and effective strategy worthy of clinical promotion.</p>