Objective To study the effect of lateral internal partial sphincterotomy and ligation on chronic anal fissure. Methods A total of 160 patients with chronic anal fissure were randomly divided into two groups. Eighty cases both in study group treated with lateral internal partial sphincterotomy combined with ligation and in control group treated with internal sphincter resection were studied. Incision size, pain score, bleeding score, anal function, hospital stay and incision would healing day on different days after operation in two groups were analyzed. Results Treatment efficacy was 100% in both groups. Cure rates was 100% in study group and 97.50% in control group (P<0.05). Incision sizes on the 1st, 3rd, 5th and 7th day after operation in study group were significantly smaller than those same-day in control group(P<0.05). Both pain score and bleeding score on the 1st, 3rd, 5th and 7th day after operation in study group were significantly lower than those same-day in control group (P<0.05). Wexner anal incontinence scores after wound healing in study group were significantly lower than those in control group(P<0.05). Hospital stay and incision wound healing day in study group were less than those in control group significantly (P<0.05). Conclusions Lateral internal partial sphincterotomy and ligation would be effective and safe in treatment of chronic anal fissure with advantages including less days of wound healing, less postoperative bleeding and pain combined with protection of anal function.