Anal fistula (AF) is a common disease with high prevalence and surgical operations are effective treatments in clinical work. There exist many well-known surgical techniques treating complex anal fistula (CAF), however, none is ideal. To compare the superiority of Anal fistula plug (AFP) and Endoanal advancement flap repair (EAFR) for complex anal fistula. We searched worldwide databases including Pubmed, Embase, Cochrane Library, Web of Science, CNKI, WanFang, VIP, and SinoMed from their inception to March 2023. Studies comparing the outcomes of AFP and EAFR were included according to the PICO principles. The indicators of the healing rate, recurrence rate, wound infection rate, and complication rate, et al. were extracted and compared between different surgical methods. 5 RCTS and 7 non-RCTs were included in the meta-analysis with a total of 847 patients (341 patients conducted with AFP and 506 patients with EAFR). By combining the total effect of the 12 articles, we found that there was a statistical difference reporting the healing rate of AFP 48.3% and EAFR 64.4% treating the CAF (OR 0.68, 95% CI 0.30,1.55, P = 0.03), and EAFR has a better healing rate. However, there was no significant difference in terms of the recurrence rate (OR 1.68, 95% CI 0.80,3.54, P = 0.17), the wound infection rate (OR 1.82, 95% CI 0.95,3.52, P = 0.07), and the complication rate (OR 1.06, 95% CI 0.70,1.61, P = 0.77) either in the 12 articles or in the subgroup. The meta-analysis indicated that the EAFR was superior to AFP in terms of the healing rate treating the CAF, however, there were no significant differences between the two groups when it came to the recurrence rate, the wound infection rate, and the complication rate. EAFR might be one initial treatment for the complex cryptoglandular anal fistulas compared with AFP.© 2023. The Author(s).