Objective To investigate the clinical effects and the brain protection effect of different cardiopulmonary bypass in treating descending aortic aneurysms. Methods From January 2001 to December 2008, 65 patients were diagnosed to have descending aortic aneurysm with magnetic resonance imaging (MRI) in our hospital. Among them, there were 56 males and 9 females whose age was between 15 and 71 years old with an average of 48.1 years. The disease process ranged from 6 days to 4 months (19.0±6.5 d ). Preoperative diagnosis showed that there were 41 cases of DeBakey type Ⅲinterlayer, 9 cases of Marfan syndrome with postoperative complications of type Ⅲ interlayer, 7 cases of pseudoaneurysm and 8 cases of true aneurysm. We adopted artificial blood vessel repair patch to repair the damaged point of the descending aorta in 2 cases, performed vascular aneurysm resection and artificial vessel replacement on 63 patients, and carried out descending aorta replacement and intercostal artery grafting in 18 cases. Results Among the 65 cases of cardiopulmonary bypass patients, there were 13 cases of left heart bypass, 12 cases of heart bypass, 30 cases of deep hypothermic circulatory arrest (DHCA) with total body retrograde perfusion (TBRP) and 10 cases of modified separate perfusion of upper and low body. Cardiopulmonary bypass time, DHCA time, retrograde perfusion time, upper body circulatory arrest time and low body circulatory arrest time were respectively 51-212 min, 18-75min, 18-73 min, 21-31 min, and 39-67 min. No death occurred during the operation, and there were no brain complications or complications of paralysis among all the patients. Two patients died after operation because of renal failure. Conclusion Good results can be achieved by selecting different method of cardiopulmonary bypass based on the anatomical location and range of the thoracic descending aortic aneurysms. The selection criteria should be favorable to the surgical operation and organ protection.