Objective To evaluate the effect of fistulotomy with seton drainage (FSD) versus traditional seton fistulotomy (TSF) in the treatment of high complex anal fistula in the elderly based on propensity score matching. Methods The clinical data of 220 patients in the Department of Anorectal Surgery of Beijing Rectum Hospital from March 2020 to March 2023 were retrospectively analyzed, including 117 in the FSD group and 103 in the TSF group. Propensity score matching was used to select a matched cohort of 82 pair (1∶1). The postoperative efficacy, recovery, pain degree, anorectal dynamics, anal canal function and recurrence were compared between the two groups. SPSS 22.0 was used for data analysis. According to the data type, t test or Chi-square test were performed for intergroup comparison. Logistic regression model was used to calculate the propensity score, and the nearest neighbor matching method was used for 1:1 matching. Results After matching at 24 h postoperatively, the visual analogue scale (VAS) score in the FSD group was lower than that in the TSF group [(4.21±1.18) vs (5.04±1.36) points], the total clinical effective rate in the FSD group was higher than that in the TSF group [96.34% (79/82) vs 87.80% (72/82)], and the wound healing time in the FSD group was shorter than that in the TSF group [(12.34±2.45) vs (14.67±2.89) d]; all the differences were statistically significant (P<0.05). At 1 month postoperatively, the FSD group had greater anal function length [(2.86±0.34) vs (2.31±0.46) cm], maximum tolerance dose [(135.21±19.87) vs (119.52±20.13) ml] and initial sensory threshold [(25.16±2.57) vs (22.89±2.92) ml] than the TSF group, and the differences were statistically significant (P<0.05). At 1 month postoperatively, the Wexner score was lower in the FSD group than that in the TSF group [(0.92±0.27) vs (1.17±0.35)pionts], and the recurrence rate in the FSD group was also lower [3.66% (3/82) vs 12.20% (10/82)]; and the difference was statistically significant (P<0.05). Conclusion FSD is effective in the treatment of high complex anal fistula in the elderly, with fast postoperative wound healing, little damage to anal canal function, and low recurrence rate.