To explore the efficacy of video-assisted anal fistula treatment (VAAFT) in treatment of complex anal fistula. Clinical data of 87 patients with complex anal fistula undergoing operation at Department of General Surgery, the Second Affiliated Hospital of Suzhou University from September 2015 to December 2016 were collected to conduct a cohort study. The operative procedure depended on economic conditions and patient preference. Patients were divided into VAAFT group (42 cases) and traditional fistula resection plus seton (FRS) group (45 cases). The procedure of FRS was to completely remove the fistula along external wall, the inner opening and surrounding scar tissues, then, the inner opening was closed with absorbable suture. For deeper and more complex fistula, the above procedure should be combined with seton. Based on the concept of endoscopic minimally invasive surgery, VAAFT could deal with the fistula and inner opening under direct vision. The brief steps were as follows: insertion of the anal fistula scope through external opening into the fistula; continuous injection of glycine-mannitol solution to expand and clean the foul fistula; electrocoagulation of all lesions; clearance of burnt tissues from the lumen with endoscopic brush and forceps; injection of medical fibrin glue through the inner opening; closing the inner opening by suture. Intraoperative and postoperative indices were compared between two groups. VAAFT group included 33 males and 9 females with mean age of (37.4±13.5) years, mean BMI of (24.3±3.2) kg/m2, and mean disease course of (4.8±3.9) months. Of 42 cases, 5 had preoperative diabetes mellitus, 31 were high fistula and 11 were low fistula. FRS group included 32 males and 13 females with mean age of (42.1±15.6) years, mean BMI of (24.8±3.7) kg/m2, and mean disease course of (5.7±3.6) months. Of 45 cases, 4 had preoperative diabetes mellitus, 37 were high fistula and 8 were low fistula. There were no significant differences in baseline data between two groups(all P>0.05). Compared with FRS group, VAAFT group had significantly shorter operative time [(44.6±10.5) minutes vs. (57.4±12.3) minutes, t=5.203, P=0.000], lower incidence of postoperative bleeding (14.3% vs. 33.3%,χ²=4.304, P=0.038), less pain (Visual Analogue Scale,VAS) (2.9±1.8 vs. 7.3±1.2, t=13.500, P=0.000), faster pain relief [(1.0±0.8) days vs. (4.5±1.2) days, t=15.890, P=0.000] and shorter hospital stay [(4.1±3.5) days vs.(7.5±2.3) days, t=5.389, P=0.000]. However, there were no significant differences between two groups in urinary retention rate, first postoperative fecal time and postoperative infection rate(all P>0.05). All patients were followed up for more than 6 months, FRS group had significantly higher incidence of anal incontinence than VAAFT group (20.0% vs. 2.4%, Fisher P=0.015). However, no significant difference in recurrence rate was found between VAAFT and FRS group(7.1% vs. 15.6%, Fisher P=0.317). Compared to traditional FRS treatment, VAAFT possesses some advantages in less injury, less pain, faster recovery, and lower postoperative anal incontinence rate. Thus, VAAFT is a superior operative choice in treatment of patients with complex anal fistula.