Objective To investigate the practical application feasibility of anatomical fistula resection in the clinical treatment of primary hospitals. Methods Eighty-eight patients with intersphincteric fistula (anal fistula) treated by surgery in Yong'an People's Hospital from January 018 to December 2022 were randomly divided into control group (even number of signs, 44 cases, anal fistula ligation) observation group (odd number of signs, 44 cases, anatomical anal fistula resection) by drawing lots. The incidence of abnormal anal function, rate of good anal morphology, the time of wound healing and VAS score (incision pain) were compared between the two groups. Results The incidence of abnormal function in the observation group was lower than that in the control group at the time of mid-healing and 6 months after healing. The time of wound healing the VAS score of pain in the observation group were lower than those in the control group. The rate of good anal morphology in the observation group was 10% after the operation, which was higher than that in the control group (84.09%), and there was a statistical difference (P<0.05). Conclusions The application of anatomical anal fistula resection in primary hospitals has a good effect on protecting anal function and repairing anal morphology.