Objective A meta-analysis was performed for a comparison of outcomes between transcatheter closure and transthoracic closure for simple congenital heart diseases (CHD). Methods Electronic databases, including PubMed, EMbase, Scopus, CNKI, Wanfang Data and Weipu Data were searched systematically for the literature aimed mainly at comparing the therapeutic effects for CHD administrated by transcatheter closure and transthoracic closure. Corresponding data sets were extracted and two reviewers independently assessed the methodological quality. The meta-analysis was conducted with Revman 5.3. Results Twelve studies meeting the inclusion criteria were included, involving 8 studies regarding to atrial septal defect (ASD), 2 studies regarding to ventricular septal defect (VSD) and 2 studies with regard to patent ductus arteriosus (PDA). A total of 1 423 patients were included. It was observed that compared with transthoracic closure, transcatheter closure entailed a lower complication rate (OR=5.62, 95%CI 2.78 to 11.36, P<0.001). However, meta-analysis of operative success rate(OR=1.65, 95%CI 0.92 to 2.98, P=0.09), instantly (OR=0.75, 95%CI 0.40 to 1.41, P=0.37) and long-term (OR=0.72, 95%CI 0.25 to 2.05, P=0.54) persistent shunt after surgery showed no significant differences between two approaches. No publication bias was found according to the funnel plot of complication rate and operative success rate. Conclusion In the treatment of simple CHD such as ASD, VSD and PDA, compared with transthoracic closure, a lower complication rate were associated with transcatheter closure. Meanwhile, operative success rate, instantly and long-term persistent shunt after surgery were not statistically different between the two surgical approaches. However, this study was based on retrospective studies, the level of evidence remained low. More large sample size randomized controlled trials should be designed to explore the safety and effectiveness of these two approaches in the treatment of CHD.