Objective To systematically review the effectiveness of thoracoscopy surgery and thoracotomy for thymoma. Methods Databases including PubMed, EMbase, The Cochrane Library (Issue 3, 2016), Web of Science, CBM, WanFang Data and CNKI were searched to collect randomized controlled trials (RCTs) and cohort studies about thoracoscopy surgery versus thoracotomy for thymoma from inception to April 2016. Two reviewers independently screened literature, extracted data, and assessed the risk of bias of included studies. Then meta-analysis was performed using RevMan 5.3 software. Results A total of 5 RCTs and 8 cohort studies involving 1 093 patients were included. The results of meta-analysis showed that, compared with thoracotomy, the thoracoscopy surgery could shorten operative time (MD= –22.2, 95%CI –32.92 to –12.52, P < 0.000 01), duration of ICU stay (MD= –0.76, 95%CI –0.21 to –0.30, P < 0.000 01), duration of hospital stay (MD= –3.71, 95%CI –4.47 to –2.96, P < 0.000 01) and duration of pleural drainage (MD= –1.80, 95%CI –2.42 to –1.18, P < 0.000 01), reduce volume of intraoperative blood loss (MD= –43.27, 95%CI –50.94 to –35.60, P < 0.000 01), and decrease the incidence of postoperative complications (OR=0.19, 95%CI 0.11 to 0.34, P < 0.000 01), but there was no significant difference in recurrence rate between two groups (OR=0.81, 95%CI 0.31 to 2.11, P=0.67). Conclusions Current evidence shows that, compared with thoracotomy, the thoracoscopy surgery for thymoma has shorter operative time, duration of ICU stay, duration of hospital stay, and duration of pleural drainage, as well as less blood loss and postoperative complications. Due to the limited quality of included studies, more high-quality studies are needed to verify the above conclusion.