Objective To evaluate the safety and efficacy of botulinum toxin type A injection around internal anal sphincter and sector resection combined with epluchage and drainage by a small incision in treatment for stage Ⅱ and Ⅲ anal fissure，explore its surgical procedures and key points，and introduce a new surgical treatment for anal fissure. Methods The patients according to the inclusive criteria were divided into trial group and control group in randomized，parallel，controlled clinical trial method．The botulinum toxin type A injection around internal anal sphincter and sector resection combined with epluchage and drainage by a small incision was performed in the trial group, the anal fissure resection and part internal anal sphinctor latero-resection was perfermed in the control group. The safety index （including anal stenosis，incontinence，acute urinary retention，postoperative pain，and rectal anal tube pressure） and validity indicators （including cure rate，operation time，wound healing，wound healing grade，and scar size） were compared before and after operation between two groups．Results No anal stenosis and acute urinary retention occurred in the two groups. The anal incontinence score was not significantly different between two groups （P＞0.05）．The postoperative pain score in the trial group was significantly lower than that in the control group （24 h，the first defecation，and on week one after operation，all P＜0.01）．The difference of rectal anal canal pressure was not statistically significant between two groups （P＞0.05）．The cure rate was higher （P＜0.05），operation time and wound healing time were shorter （P＜0.01），wound healing was better （P＜0.05），scar area was smaller （P＜0.01） in the trial group as compared with the control group．Conclusions Comparing with the control group，high cure rate，short wound healing time，small size of scar，short operation time and minimal invasion are seen in the trial group．The shape and function of the anus are better reserved than that of the control group，this technique has a good clinical efficacy and safety．