The overlap between high-speed railways and earthquake areas makes it necessary to implement isolation design for railway bridges. At present, the variation of seismic energy of railway bridges with structural and ground motion parameters is not clear. In this paper, the finite element models of railway bridges with different pier heights are established and verified by shaking table tests. Then, the nonlinear time history analysis of isolated and non-isolated models is carried out, and the differences in seismic response and energy dissipation between the two models under different parameters are compared. Finally, the isolation effect of hyperbolic friction pendulum bearing (HFPB) is evaluated by using the efficacy coefficient method. Results demonstrate that HFPB can not only reduce the seismic response of the girder and the pier, but also effectively reduce the seismic input energy, structural damping energy, and pier hysteretic energy. In addition, HFPB has a better seismic isolation effect when pier height is 3–15 m, site characteristic period is 0.25–0.45 s, and earthquake PGA is 0.2–0.5 g.