Hemodynamics in aortic dissection (AD) is closely associated with the risk of aortic aneurysm, rupture, and malperfusion. Altered blood flow in patients with AD can lead to severe complications such as visceral malperfusion. In this study, we aimed to investigate the effect of cannulation flow on hemodynamics in AD using a fluid–structure interaction simulation. We developed a specific-idealized AD model that included an intimal tear in the descending thoracic aorta, a re-entry tear in the left iliac artery, and nine branches. Two different cannulation methods were tested: (1) axillary cannulation (AC) only through the brachiocephalic trunk and (2) combined axillary and femoral cannulation (AFC) through the brachiocephalic trunk and the right common iliac artery. AC was found to result in the development of a pressure difference between the true lumen and false lumen, owing to the difference in the flow rate through each lumen. This pressure difference collapsed the true lumen, disturbing blood flow to the celiac and superior mesenteric arteries. However, in AFC, the pressure levels between the two lumens were similar, and no collapse occurred. Moreover, the visceral flow was higher than that in AC. Lastly, the stiffness of the intimal flap affected the true lumen's collapse.