This research investigated the effect of different nano-biological scaffolds on blood vessel walls by numerical analysis. The dynamics behavior of fluids and the mechanical property of vessel wall were studied when the blood vessel wall was in the state of inflammation. Employing straight and bent blood vessels as 3D models, this research simulated the blood flow in the inflammatory blood vessels and put forward the mathematical method to analyze mechanical characteristics of the vessel walls under the condition of the bi-directional coupling. At the same time, the impact of the nano-biological scaffolds was explored. The results showed that the thrombus in the inflammatory blood vessels significantly influenced the dynamics behavior of blood fluids. The blood velocity in the rectangular mesh nano-biomaterials was greatly decreased. It concluded that the numerical method was feasible to estimate signal feedbacks. Simulating the fluid dynamics behavior in the inflammatory blood vessels, the mechanical characteristics of the vessel wall under the condition of the two-way coupling was consistent with the medical facts. Moreover, the clogging degree had significantly influence on the inflammation of vessel wall. These findings facilitated health care workers to employ proper nano-biological scaffolds in the thrombosis treatment.