Objective To evaluate the efficacy and safety of transthoracic minimally invasive occlusion operation for the treatment of congenital atrial and ventricular septal defects. Methods The clinical data of 88 patients who underwent surgical occlusion operation from December 2015 to February 2017 were summarized. There were 52 males and 36 females, aged 6.8±7.5 years ranging from 1.6 to 24.0 years. All the patients were followed up by ultrasound and electrocardiogram at postoperative 3, 6 and 12 months. The efficacy of minimally invasive thoracotomy was analyzed by statistical methods. Results The patients were followed up for 3-15 (6.8±2.3) months, and the follow-up rate was 92.0%. Ultrasound showed occluder fixed well and no residual shunt, valve regurgitation, thrombosis or other complications occurred. The heart was reduced, the ejection fraction was greater than 55%, and heart function rating for all patients was grade Ⅰ. Conclusion Transthoracic mini-invasive surgical occlusion of atrial and ventricular septal defects is safe and effective. The short and middle-term effect is satisfying. It can be widely used in clinical, but multi-center and long-term follow-up and assessment still need to be carried out.