Intersphincteric resection (ISR) involves the anatomy of hiatal ligament, internal and external sphincter and conjoined longitudinal muscle. The hiatal ligament is actually a branch of the longitudinal muscle of rectum, shown as an uneven ring attached to the levator ani muscle. The internal sphincter is the end of the circular muscle of rectum which begins at the level of hiatal ligament formation. The distance from the upper boundary of internal sphincter to dentate line is significantly different among individuals. Although there is adipose tissue in the space between the internal and external sphincters, no evidence of mesentery structure in the anal canal is found as in the rectum. The conjoined longitudinal muscle is the remaining branch of the longitudinal muscle, whose return passes through the external sphincter and ends at the anococcygeal ligament/coccyx after reaching the anal margin. The synergistic action of conjoined longitudinal muscle and the hiatal ligament participates in the defecation process. The individualized difference of ISR-related anatomy affects the operation, especially the anastomosis.