The interaction of aortic wall characteristics and cardiac function in Fontan patients is unclear. 4D flow MRI was employed to quantify the wall shear stress (WSS) and oscillatory shear index (OSI) in the aorta. Fontan patients exhibited increased axial WSS, decreased axial OSI and non-roundness of WSS in descending aorta (DAo). We also found that the increased axial WSS in DAo correlated with decreased ejection fraction and increased indexed end-systolic volume. The cardiac dysfunction presented adverse interaction with aortic wall characteristics in patients with Fontan, especially in DAo, and might lead to higher risk of atherosclerosis and stenosis.