ObjectiveTo understand progress of stem cell transplantation in treatment of complex anal fistula.MethodThe relevant literatures were searched in the PubMed, Web of Science, CNKI, Wanfang, and other databases and the clinical efficacy, advantages and problems of the therapy were analyzed and summarized.ResultsThe stem cells currently used in the field of complex anal fistula were mainly the adipose tissue-derived stem cells, which had the biological characteristics of regenerative differentiation, immune regulation, and repair of intestinal mucosal barrier, which could be used as the seed cells for the treatment of complex anal fistula, its effectiveness was worthy of recognition. But its long-term clinical efficacy remained to be seen due to its clinical treatment options were different and lack of uniform standards. The safety of treatment for complex anal fistula was payed a attention because the stem cells had the oncogene activation and tumor suppressor gene inactivation characteristics.ConclusionsStem cell transplantation, as an emerging therapy, has broad prospects for patients with complex anal fistula that are difficult to solve by surgery, but its long-term efficacy is still unsatisfactory. Due to current sample size, short observation time, and lack of randomized control, current clinical data is not convincing, and high cost also limits its development of technology.