Objective To investigate the safety and effectiveness of the operation of integrate subparagraph, fenestration, exclusion, cut expansion, seton, tube, and drainage (ISFECSTD) to cure complex anal fistula. Methods Using randomized comparison and multicenter parallel experiment, the total number was 240: 120 patients in study group treated by ISFECSTD, and 120 patients in control group treated by extended cutting and seton operation. Then compared the safety and effectiveness between two groups. Results The clinical recovery rate of the study group was significantly higher than that in the control group （Plt;0.05）. The operation time and wound healing time in study group were significantly less than those in control group, and the scar area after wound healing was smaller than that in control group （Plt;0.01）. The decreased extents of anorectal pressures and rectal capacity feeling function after operation in study group were smaller than those in control group (Plt;0.01). Rectal and anal reflex function and healing of the endostoma, stem, and branch in study group were better than those in control group (Plt;0.05, Plt;0.01). Incidence of anal incontinence after operation in study group was significantly less than that in of anus-rectum structure and function, and has the merits of higher cure rate, shorter time of healing, smaller scar, less pain, etc. The method of ISFECSTD is worth being a new standardized operation in the clinical application.