This study aimed to compare the efficacy between decompression and drainage seton (DADS) and cutting seton (CS) in the treatment of high complex anal fistula. Patients were randomly assigned 1:1 to DADS or CS group. The primary outcome was the rate of wound healing. Second outcomes included time taken to return to work, postoperative pain, the severity of fecal incontinence and other complications. A total of 120 patients with a mean age of 39 years were included. There was no significant difference in the rate of complete wound healing at 1 year. The mean time taken to return to work was 5 +/- 2 days in DADS group, shorter than CS group (10 +/- 3, p < 0.001). Mean vaizey incontinence score and the post-operation pain in DADS group was significantly lower than CS group. No significant difference was found between two groups in the incidence of complications. DADS is as effective as Cutting seton for the treatment of high complex anal fistula but is associated with less postoperative pain and better sphincter function preserving.