Objective To systematically investigate the clinical efficiency and safety of ligation of inter sphincteric fistula tract versus incision-thread-drawing procedure for complicated anal fistula. Methods Searched PubMed, The Cochrane Library, CNKI, WanFang Data, and VIP from inception to May 2016, to collect randomized controlled trials of ligation of inter sphincteric fistula tract versus incision-thread-drawing procedure for complicated anal fistula. Search term included ligation of inter sphincteric fistula tract, fistula, incision-thread-drawing procedure, randomized controlled trial. The literatures were screened according to inclusive criteria, data were extracted and the quality of included studies was evaluated, and then meta-analysis was performed using RevMan 5.2 soft ware. A total of 5 randomized controlled trials including 305 patients were included. Results The results of meta-analysis showed that compared with incision-thread-drawing procedure, ligation of inter sphincteric fistula tract had a significant difference in amount of bleeding during surgery (MD=-18.30, 95%CI: -19.91~-16.69, P<0.000 01), the duration of pain (MD=-4.38, 95%CI: -4.69~-4.08, P<0.000 01), healing time (MD=-10.28, 95%CI: -15.71~-4.86, P=0.0002), hospital stay (MD=-7.44, 95%CI: -10.87~-4.02, P<0.000 1), recurrence rate (OR= 0.31, 95%CI: 0.10~0.91, P=0.03). There was no significant difference in Operation time (MD=-5.83, 95%CI: -7.64~-4.02, P<0.000 01), effective percentage (OR=4.35, 95%CI: 0.89~21.32, P=0.07) between both groups. Conclusion Compared with incision-thread-drawing procedure, ligation of inter sphincteric fistula tract shows significant advantage in cure rate, postoperative healing time, reducing post-operation pain, anal function protection and recurrence rate. Key words: Rectal fistula; Randomized controlled trial; Meta-analysis; Ligation of intersphincteric fistula tract; Incision-thread-drawing procedure