Murine models have been widely used to investigate the mechanobiology of aortic atherosclerosis and dissections, which develop preferably at different anatomic locations of aorta. Based MRI and finite element analysis with fluid–structure interaction, we numerically investigated factors that may affect the blood flow and structural mechanics of rat aorta. The results indicated that aortic root motion greatly increases time‐averaged wall shear stress (TAWSS), oscillatory shear index (OSI), relative residence time (RRT), displacement of the aorta, and enhances helical flow pattern but has limited influence on effective stress, which is highly modulated by blood pressure. Moreover, the influence of the motion component on these indicators is different with axial motion more obvious than planar motion. Surrounding fixation of the intercostal arteries and the branch vessels on aortic arch would reduce the influence of aortic root motion. The compliance of the aorta has different influences at different regions, leading to decrease in TAWSS and helical flow, increase in OSI, RRT at the aortic arch, but has reversed effects on the branch vessels. When compared with the steady flow, the pulsatile blood flow would obviously increase the WSS, the displacement, and the effective stress in most regions. In conclusion, to accurately quantify the blood flow and structural mechanics of rat aorta, the motion of the aortic root, the compliance of aortic wall, and the pulsation of blood flow should be considered. However, when only focusing on the effective stress in rat aorta, the motion of the aortic root may be neglected.

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