An 11-month-old girl with an unbalanced atrioventricular septal defect, coarctation of the aorta and an interrupted inferior vena cava with hemiazygos continuation post-surgical status of coarctation repair and pulmonary artery banding underwent a Kawashima operation. Severe hypoxia occurred immediately after she was weaned from cardiopulmonary bypass, which was successfully resolved by the ligation of the hemiazygos vein. Postoperative enhanced computed tomography detected significant venovenous malformation from the hemiazygos vein to the left renal vein.