Objective To trace and review the treatment of complex anal fistula so as to consider whether current procedures and therapies might offer a better choice. Methods Through the literature collected, with the difficulties and contradictions of the treatment of complex anal fistula as the starting point, the currently widely used seton management, the development and deficiency of biological therapy and sphincter preserving surgery, and the change of treatment model of complex anal fistula were reviewed. The research progress and application prospect of intersphincteric fistula ligation was focus attented. Results The treatment of complex anal fistula would be not too much emphasis of healing or radical cure, and more attention to the anus function, shape, fine feeling, and quality of life, has become a consensus. The seton management remained an useful therapy for the treatment of complicated anal fistula through continuous improvement and development, in despite of it has postoperative relapse or mild to moderate anal incontinence. Biotherapy relied on its minimal invasion rising in recent years especially at abroad, but it is limited wider application in China because of its high cost, unstable efficacy, and high recurrence rate. Sphincter-preserving operation always attracts attentions particularly under the background of invasive treatment. It has been already established about efficacy and security of the ligation of intersphincteric fistula tract as a novel procedure, which possessed an excellent advantage for protecting anal continence. Conclusion The ligation of intersphincteric fistula tract is a promising procedure, which tends to be superior than fistulotomy and seton management, may become a first-line treatment of complex anal fistula.