Objective To observe and compare the clinical effects of modified LIFT on anal fistula. Methods One hundred anal fistula patients receiving surgical treatment were divided into a control group and an observation group, with 50 cases in each group. The control group received traditional surgical treatment, while the observation group received modified LIFT surgery. The clinical efficacy, postoperative anal function, and complications of the two groups were retrospectively analyzed and compared. Results The total effective rate of the observation group was higher than that of the control group （98.00% vs. 82.00%, P<0.05）, the anal function 1 and 2 months after surgery was better （P<0.05）, and the incidence rate of complications was lower （2.00% vs. 26.00%, P<0.05）. Conclusion Compared with the traditional surgical method, the modified LIFT surgery has a significant effect on anal fistula with improved postoperative anal function and reduced risks of complications, which is worthy of clinical promotion.