Milling of the low rigidity and large deformation thin-walled workpiece is a critical challenging task due to the obvious machining vibration, which greatly affects the machining accuracy, surface quality of the final part. Compared with the conventional methods, this paper focuses on suppressing the machining vibration of the flexible workpiece by the MR damping fixture. A novel dynamic characteristics reconstruction strategy of MR damping fixture-workpiece system is proposed to improve the system dynamic characteristics of milling system considering the effect of material removal. Then, the fixture-workpiece system dynamic characteristics reconstruction model is established, in process, the time-varying modal parameters in different conditions are iteratively identified and the stable depth of cut is obtained in any moment. Based on this, the control currents of MR damping fixture are calculated to offset the change of the damping and stiffness properties of the milling system caused by material removal. Subsequently, the feasibility and effectiveness of the proposed method are validated by several experiments. Experimental results show that compared with the initial machining state, the dynamic properties of the fixture-workpiece system are reconstructed by the MR damping fixture, and the vibration response is reduced by 30%~70% and the machined surface is improved effectively.