Objective To compare the long-term efficacy and complications of peroral endoscopic circular myotomy and full-thickness myotomy for patients with achalasia. Methods A retrospective analysis was performed on the clinical data of 53 patients with achalasia, who underwent peroral endoscopic myotomy in the First Affiliated Hospital of Zhengzhou University from June 2012 to December 2014 and were followed-up regularly．Twenty-one patients underwent circular myotomy, and the other 32 patients underwent full-thickness myotomy. The postoperative long-term efficacy and gastroesophageal reflux complications of the two groups were compared．Results The effective rate of the circular myotomy group and the full-thickness myotomy group was 90.5% (19/21) and 100% (32/32)，respectively. There were no significant differences between the two groups on postoperative Eckard scores, lower esophageal sphincter pressure and 4 s integrated relaxation pressure. The incidence of clinically relevant gastroesophageal reflux of full-thickness myotomy group was higher than that of circular myotomy group (40.6% VS 14.3%, χ2=4.174, P=0.041). Conclusion The long-term efficacy of circular myotomy is similar to that of full-thickness myotomy, but the incidence of clinically relevant gastroesophageal reflux is higher in full-thickness myotomy.