Objective To analyze and compare the clinical efficacy and advantage between two treatments methods for chronic anal fissure. Methods Divided 96 patients with chronic anal fissure into two groups based on the odd and even numbers of treatment order: 48 patients in study group received sequential anal dilation and microwave treatment, and 48 patients in control group received posterior internal sphincterotomy. The blood loss in operation, wound healing time, wound infection rate, anal infection rate, anal control, postoperative defecation function, anal stenosis rate, and the recurrence rate between the two groups were compared and analyzed. Results Blood loss and wound healing time were less in study group than those in control group (Plt;0.01). Anal control was better in study group than that in control group (Plt;0.05). There were no occurrences of wound infection or anal infection, and the defecation function was improved in both of the two groups. There was no recurrence after one year follow-up in both of the two groups. Anal stenosis rate in study group is lower than that in control group (Plt;0.01). Conclusion The technique of sequential anal dilation and microwave treatment can reduce pain, and is simple, effective, and worthy of promotion.