Interactions of ET-1 (Endothelin-1) with its receptors ETA (Endothelin-A) and ETB (Endothelin-B) regulate the vascular tone, maintain the blood pressure, and are closely related to cardiovascular diseases. Binding of ET-1 with ETB in the vascular endothelium induces vasodilation, while binding with ETA and ETB in vascular smooth muscle results in vasoconstriction. Because ET-1 only induces vasodilation in vivo when the blood flow is present, we speculate that the shear stress of the blood flow may control the conformation of ET-1 through its structural flexibility, thus regulate its binding with ETB. By flow molecular dynamics simulation, the conformational changes of ET-1 in uniform flow were studied with its center of mass constrained. It is found that the C-terminal of ET-1 gets closer to the N-terminal in the simulation, resulting in a compact structure. This finding may provide guidance for the study on the interaction between ET-1 and ETB and the design of ET-1-based cardiovascular drugs.