Rubber isolation bearings have been proven to be effective in reducing the seismic damage of bridges. Due to the different characteristics of isolation bearings, the mechanical properties of bridges with different combinations of rubber bearings are complex under the action of earthquakes. This paper focuses on the application of combinations of rubber isolation bearings on seismic performance of continuous beam bridges with T-beams. The seismic performances of continuous beam bridges with different combinations of rubber isolation bearings, pier height, and span length were studied by the dynamic time history analysis method. It was found that the bridges with natural rubber bearings (NRBs) have the largest seismic responses compared to the other types of bearings. The continuous beam bridge with isolation bearings, such as lead rubber bearings (LRBs) and high damping rubber bearings (HDRBs), has approximately 20%∼30% smaller seismic response than that with NRBs under the action of earthquakes due to the hysteretic energy of the bearings, indicating that the isolation bearings improve the seismic performance of the bridge. The continuous beam bridges with both NRBs and LRBs or NRBs and HDRBs have larger seismic response of the piers than those with a single type of isolation bearings (LRBs or HDRBs) but smaller seismic response of the piers than those with only NRBs. For a continuous beam bridge with shorter span and lower pier, it is not economical to use LRBs or HDRBs underneath every single girder, but it is more reasonable to use cheaper NRBs underneath some girders. The larger difference in stiffness of the bearings between the side and middle piers leads to the more unbalanced seismic response of each pier of the bridge structure. The results also show that with increasing pier height and span length, the difference in the seismic response value between the cases gradually increases.