This is one case report of a 46-year-old Chinese male with type A acute aortic dissection. It is an emergent surgery including Bentall procedure, interposition graft replacement of aortic arch, stented descending aorta with the modified right atrial shunt technique. In the early post operation period, the patient was complicated with pulmonary embolism. Pulmanary arteriography showed that the right main pulmonary embolism without an extrinsic compression. After the anticoagulant therapy, the patient was well recovered and discharged from hospital 1 month later. The origin of pulmonary embolism in the patient was believed to be the thrombosis in the shunt fistula. The right atrial shunt-related complications haven't been reported for more than thirty years. Pulmonary embolism could be a severe complication after the right atrial shunt in acute type A aortic dissection.