Objective Based on clinical surgical statistical instances, the influence of double fenestration branch stents on the blood flow field after different depths of implantation in the diseased thoracic aorta was investigated. Methods Thoracic aorta, thoracic aorta-coated stent, and branch vessel-coated stent were established. The finite element calculation method was used to analyze the branch stent implanted into the diseased aorta at different depths (5, 10, and 15 mm), and experimental verification was performed using an in vitro tachymetry experimental platform. Results There were certain patterns for maintaining stable perfusion of the blood flow field with branch stent implantation at different depths in the thoracic aorta. The branch blood perfusion rate in Group D10-5 (the implantation depths of the left common carotid artery branch stent and left subclavian artery branch stent were 10 mm and 5 mm, respectively) was at a good level, and TAWSSmax was at the lowest level (44.94 Pa), thereby showing the best simulation results. Conclusions When the left subclavian artery branch stent implantation in the thoracic aorta was short, the depth of the left common carotid artery branch stent implantation in the aorta was appropriately increased to obtain a more stable blood flow field. This study provided a theoretical reference for the double-fenestration technique in clinical practice.