In this study the effectiveness of Polynomial Friction Pendulum Isolators (PFPIs) for the isolated bridge with columns of irregular height is investigated using shaking table testing. A single-span model bridge was designed and built, and two sets of PFPI prototype isolators were fabricated. Compared with typical isolated bridges, the isolated bridges with columns of irregular heights result in different seismic response at each column. The experimental results show that the hysteresis loops of the prototype PFPIs agree well with the theoretical ones predicted by numerical simulation. The analytical displacements are almost identical to the experimental data. Moreover, the test results also demonstrate that when the parameters of the PFPIs are proportionally designed, the PFPIs are able to effectively decrease the maximum shears at the base of the irregular columns which are induced by a near-fault earthquake. In addition, it is difficult to determine the parameters of the PFPIs at each irregular column. The PSO-SA hybrid searching algorithm is thus adopted to explore the optimum parameters of the PFPIs through numerical analysis. With the proper selection of the objective function, the maximum moment at the base of each column can be uniform satisfactorily.