This paper aimed at evaluating the influence of different vertical equivalent damping ratios of a 3-dimensional combined isolation bearing (3D-CIB) as regards seismic response and isolation effectiveness. A comparative study of the seismic response in terms of acceleration floor response spectra (FRS), peak acceleration, displacement response of the nuclear reactor building, and dynamic response of the 3D-CIB was carried out. The results showed that: (1) the horizontal FRS is slightly influenced by the vertical equivalent damping ratio of 3D-CIB, whereas the increase of the vertical equivalent damping ratio has a significant effect on reducing the vertical FRS; (2) the peak vertical acceleration increased with the decrease in the vertical equivalent damping ratios of 3D-CIB and the difference of peak accelerations calculated by the damping ratio of 20 and 25% is within 10%; (3) the increase of the vertical equivalent damping ratio is capable of reducing the horizontal displacement and the rocking effect of the superstructure, and effectively controlling the vertical displacement amplitude; and (4) the vertical equivalent damping ratio of 3D-CIB has a slight effect on its axial force. Consequently, it is demonstrated that the increase of the vertical equivalent damping ratio is advantageous for isolation effectiveness. From the view of displacement control, it is suggested that the 3D-CIB with the vertical an equivalent damping ratio of 15~20% is appropriate and acceptable.