This report describes changes in the treatment strategy for transposition of the great arteries (TGA) undergoing primary arterial switch operation early in the neonates in our institution. Decrease in pulmonary vascular resistance after birth results in deterioration of left ventricular (LV) performance as a systemic ventricle and right ventricular (RV) failure. Ductus arteriosus should be kept patent by alprostadil alfadex (PGE1) in order to prevent deterioration of LV performance. Contrarily, pulmonary high flow leads to the progression of RV failure. Balloon atrial septostomy (BAS) and PGE infusion may be helpful to manage severe hypoxemia, but an increase in aortic septal defect (ASD) flow may lead to deterioration of LV performance. To solve these dilemma primary arterial switch operation should be underwent as early as possible.