A magnetorheological elastomer (MRE) is one of smart materials which can control the stiffness according to the magnetic field strength. Various types of MRE-based isolators have been studied. However, there was a limit to performance validation owing to the material and structural limitations. In this study, an optimal mixing ratio of the MRE was considered, and a novel electromagnetic system was proposed. A multi-layered electromagnetic system was proposed to constantly maintain a closed magnetic circuit by acting on the deformation of the MRE. As a result, numerical and experimental comparisons were performed with the conventional MRE-based isolator, and its superiority was validated. Moreover, the dynamic characteristics of the proposed MRE-based isolator under a vertical load were investigated. The results show that the proposed MRE-based isolator outperforms the conventional MRE-based isolator in improving the magnetorheological (MR) effects and the dynamic characteristics of the proposed MRE-based isolator under the vertical load were identified.