The buildings located near or on top of the railway systems are generally affected by the rail-induced vibration. Vertical vibration isolation is an effective measure to reduce the influence of rail transit vibration. However, the vertical isolated structures are prone to overturning moment which can result in rocking of the superstructure under earthquake. To resolve this issue, three-dimensional (3D) vibration isolation which involves a system that combines both the vertical vibration isolation and horizontal seismic isolation is proposed. This study carried out a shaking table test to compare the rocking behaviour of a vertical isolated structure and a 3D isolated structure. The testing structure was a three-story steel frame structure, with an aspect ratio of 3.3, and the vibration isolation bearings were installed under the column bases. Test results demonstrated that the rocking amplitude of the vertical isolated structure was about 2 times of the non-isolated conventional structure. While the horizontal accelerations and rocking amplitudes of the 3D vibration isolated structure were about 70% smaller than the structure with only vertical vibration isolation. This study verified the effectiveness and necessity of 3D vibration isolation in the rail-induced vibration control.