The high-speed railway (HSR) system imposes stringent requirements for track smoothness. However, conventional seismic isolation bearings frequently fail to meet these demands. To address this challenge, a novel seismic isolation bearing was developed based on the principle of functional separation design. This innovative bearing effectively achieves the multistage control objectives, including amplitude limitation to ensure track smoothness during frequent earthquakes, energy dissipation to guarantee train running safety during design earthquakes, and structural integrity maintenance to prevent beam collapse during rare earthquakes. Firstly, an overview of the novel isolation bearing’s structural design and operational principle is provided. Subsequently, a corresponding mechanical model is formulated, with the parameters of the new bearing determined through finite element analysis. The study then compares the seismic performance of the general rubber bearing and the new bearing, using an HSR simply supported bridge as an engineering background. The dynamic response of the bridge under varying seismic waves, pier heights, and bridge spans is meticulously analyzed. The results indicate that the new bearing can achieve multistage control. Compared to general bearings, it reduces bridge displacement vibration by over 46.4% under frequent, design, and rare earthquakes. The bridge deformation under frequent earthquakes remains below 3 mm, thus meeting the track smoothness requirements for normal HSR operations. Additionally, the study reveals that higher pier heights increase the seismic response, peaking at 15 m. The vibration reduction provided by the new bearing varies but remains effective in most earthquake scenarios, with maximum reductions of 92.9% for displacement and 74.17% for bending moment. Furthermore, larger bridge spans also increase the seismic response, with the 24 m span bridge outperforming the 32 m span bridge. In conclusion, the novel seismic isolation bearing significantly enhances the seismic performance of HSR bridges, ensuring train running safety and operational reliability.