Objective To summarize the clinical experience in surgical management of transposition of the great arteries with intact ventricular septum (TGA/IVS). Methods One hundred and nineteen patients with TGA/IVS were divided into emergency operation group (n=61) and selected operation group (n=58), and patients were subjected to arterial switch operation (ASO)(emergency operation group, n=58; selected operation group, n=54, including 14 cases of second stage ASO), systemic-pulmonary shunt and pulmonary artery banding (emergency operation group, n=2; selected operation group, n=14) or Senning operation (emergency operation group, n=1; selected operation group, n=4). The operation and follow-up results were observed and compared between two groups, and univariate Logistic regression analysis was performed to determine the influencing factors for mortality early after operation. Results Twelve patients died in hospital after operation (10.1%), and the mortality of emergency operation group was higher than that of selected operation group, while there was no significant difference between two groups (14.8% vs 5.2%, P=0.08). Univariate Logistic regression analysis revealed that the risk factors for mortality early after operation were emergency ASO and preoperative left ventricle mass (LV Mass)≤50 g/m² (P＝0.05，P＝0.00). Eighty-three survivors were followed up for 3 months to 4.5 years, during which no death occurred, and 1 patient underwent reoperation for supravalvular pulmonary stenosis. Conclusion Surgical management of TGA/IVS may yield good results, and application of balloon atrial septostomy and assisted circulation may further decrease the mortality after operation.