A newborn male was admitted with cyanosis and respiratory distress. Echocardiography showed a right heart isomerism associated with a single right ventricle, a double-outlet right ventricle, and pulmonary atresia. Chest X-ray demonstrated severe left upper lobe emphysema and a shift of the mediastinal structures to the right. Two-dimensional computed tomography (CT) exhibited left upper lobe emphysema and right upper lobe atelectasis. Three-dimensional (3D) spiral CT angiography showed a bilateral tracheal bronchus. The left tracheal bronchus branch was compressed between the descending aorta and the ductus arteriosus. After a right arteriopulmonary shunt operation, the patient's respiratory condition improved dramatically, with spontaneous closure of the ductus arteriosus. Subsequently, 3D-CT clearly exhibited the disappearance of tracheal compression. This combination of bilateral tracheal bronchus and congenital heart anomaly is extremely rare. The 3D-CT is a powerful noninvasive means for dynamically demonstrating the special relationships of arterial and tracheal anomalies.