Criss-cross heart is an extreamly rare anomaly characterized by abnormal rotation of the heart on its long axis. Almost always there are associated cardiac anomalies such as pulmonary stenosis, ventricular septal defect (VSD) and ventriculoarterial connection discord, and most cases are candidates for Fontan procedure due to hypoplasia of right ventricle or straddling atrioventricular valve. We report a case of arterial switch operation for criss-cross heart with muscular ventricular septal defect. The patient was diagnosed with criss-cross heart, double outlet right ventricle, subpulmonary VSD, muscular VSD and patent ductus arteriosus (PDA). PDA ligation and pulmonary artery banding (PAB) was performed in the neonatal period, and an arterial switch operation (ASO) was planed at 6 months of age. Preoperative angiography showed nearly normal right ventricular volume and echocardiography showed normal subvalvular structures of atrioventricular valves. ASO, intraventricular rerouting and muscular VSD closure by sandwitch technique were successfully performed.