The feasibility of using MR fluids to develop a smart material-structure system and thereby to prevent structure from catastrophic damage is actively carried out in this study. The MR smart fluids are utilized to develop a smart damper with controllable parameters and the mechanical model of MR devices is presented by involving the effects of damper's axial stiffness. The interaction of a smart material-structure system is analyzed through the numerical integral and iteration. The vibration mitigation of the dynamic responses of an engineering structure with the smart coupled system is conducted based on the intelligent fuzzy control for performance evaluation. It is observed that the structural internal forces such as shear forces and bending moments can be remarkably mitigated with the protection of the smart system.