Objective    To compare the clinical efficacy of endoscopic minimally invasive surgery and median sternotomy thoracotomy in the treatment of atrial myxoma by meta-analysis. Methods    We searched CBM, CNKI, Wanfang Data, VIP, PubMed, the Cochrane Library and EMbase to collect relevant researches on atrial myxoma and endoscopic minimally invasive surgery. The retrieval time was from the establishment of the database to September 2020. Two reviewers independently screened the literature, extracted data and evaluated the bias risk of included studies by the Newcastle-Ottawa scale (NOS). Then, the meta-analysis was performed by Stata 16.0. Results    Ten articles were included in the study, all of which were case-control studies. The quality of literature was grade B in 5 articles and grade A in 5 articles. The sample size of surgery was 938 patients, including 480 patients in the endoscopic minimally invasive group, 458 patients in the median thoracotomy group, and 595 patients in follow-up. A total of 18 outcome indexes were included in the meta-analysis. The combined results of 9 outcome indicators were statistically significant: cardiopulmonary bypass time (SMD=0.32, 95%CI 0.00 to 0.63, P=0.048); ventilator assisted ventilation time (SMD=−0.35, 95%CI −0.56 to −0.15, P=0.001), ICU stay time (SMD=–0.42, 95%CI −0.62 to −0.21, P<0.001); postoperative hospitalization time (SMD=−0.91, 95%CI −1.22 to −0.60, P<0.001); postoperative drainage volume (SMD=−2.48,  95%CI −5.24 to 0.28, P<0.001); postoperative new onset atrial fibrillation (OR=0.29, 95%CI 0.12 to 0.67, P= 0.005); postoperative pneumonia (OR=0.09, 95%CI 0.02 to 0.36, P=0.001); postoperative blood transfusion (OR=0.22, 95%CI 0.11 to 0.45, P<0.001); incision satisfaction (OR=83.15, 95%CI 1.24 to 5 563.29, P=0.039). Conclusion    Available evidence suggests that median thoracotomy requires shorter cardiopulmonary bypass time than endoscopic minimally invasive surgery; during the 5-year follow-up after surgery and discharge, ICU stay time, postoperative hospital stay, postoperative drainage, new atrial fibrillation after surgery, postoperative pneumonia, postoperative blood transfusion, satisfactory incision, endoscopic minimally invasive surgery showed better results than median sternotomy thoracotomy.