To investigate the isolation effectiveness of high-performance isolation rubber bearing (HIRB) on the small-to-medium span girder bridges in mountainous areas, shaking table tests were conducted on a two-span continuous girder bridge model in longitudinal direction. The model had different pier stiffness and was isolated by HIRB. Artificial earthquake waves and Northridge waves with multi intensities were applied as input ground motions. By studying HIRB’s deforming performance and measured structural response under various excitations, it is found that HIRB could mitigate the girder acceleration by 58% at most compared with input peak ground acceleration (PGA) and could roll over stably to satisfy the relative displacement between girder and piers under E2 earthquakes of 9-degree intensity with no residual displacement. Test results indicate the feasibility and effectiveness of applying High-Performance Isolation Rubber Bearing in continuous girder bridges with different pier heights.