Surgical pulmonary embolectomy is indicated for acute massive pulmonary thromboembolism complicated by floating thrombi in the right heart system. Postoperative residual thrombi are associated with persistent pulmonary hypertension and subsequent right heart failure, resulting in poor surgical outcome. A 67-year-old man was admitted to our institution owing to dyspnea on exertion. Transthoracic echocardiography revealed a floating right atrial mass and right ventricular overload. In addition, enhanced computed tomography (CT) showed a right atrial mass as well as bilateral massive pulmonary embolism. We performed an urgent pulmonary embolectomy using a bronchoscope as an adjunctive angioscope to completely remove the peripheral thrombi and to prevent serious complications, such as endobronchial hemorrhage due to pulmonary arterial injury. A clear, bloodless view of peripheral pulmonary arteries was obtained using short intermittent circulatory arrest technique. Postoperative course was uneventful, and he was discharged ambulatory 20 days after the surgery without any symptoms.