Magnetorheological elastomer (MRE), as a field-dependent smart material, has been widely applied on base isolation for vibration reduction. However, the MRE isolation system often experiences large drift during a strong earthquake, which may cause mechanical failure. Additionally, its performance among the low-frequency range is still limited. To tackle these problems, this paper proposes a hybrid vibration isolation system which is composed of four stiffness softening MRE isolators and a passive ball-screw inerter. A simulation was developed to prove the effectiveness of the hybrid isolation system before the earthquake tests. A scaled three-storey building was developed based on the scaling laws as the isolated objective in earthquake experiments. Besides, a linear quadratic regulation controller was utilised to control the mechanical properties of the hybrid MRE isolation system. Finally, the evaluation experiments of the building under a scaled Kobe earthquake excitation were conducted. The experimental results show that the simulation and the experimental results were in agreement, validating that the hybrid isolation system could provide a better vibration mitigation performance, in the meanwhile, reduce the displacement amplitude of the isolation system.