ObjectiveThe aim of this analysis was to compare the advantages of the anal fistula plug (AFP) with the mucosa advancement flap (MAF) for complex anal fistulas.MethodsComparative studies of the efficacy of AFP and MAF were included. Two independent reviewers selected articles for inclusion. After information collection, a meta‐analysis was performed using data on overall healing rates, complications, incontinences and recurrences. The quality of postoperative life and cost were also included with the clinical results.ResultsTen studies included 778 patients who were divided into AFP and MAF groups in this meta‐analysis. During the follow‐up period, no significant difference in healing rates, complications and recurrences were found (P = 0.55, P = 0.78 and P = 0.23, respectively). The incontinence rate of AFP was lower than that of MAF (P = 0.04). The postoperative quality of life of AFP patients was superior to that of MAF patients. The AFP patients had less persistent pain of a shorter duration and shortened healing time and hospital stay. The treatment cost of AFP patient was lower than that of MAF.ConclusionCompared to the MAF procedure, the AFP procedure has some advantages for complex anal fistulas, but more and large randomized clinical trials comparing the two procedures for fistula management need to be conducted.