In order to obtain a reasonable seismic isolation system for typical high-speed railway simply supported bridge in nine-degree seismic regions, an analysis method for seismic hazard contribution parameter of bridge site was proposed, and a calculation method for seismic vulnerability of bridge was deduced by using kernel density estimation theory, then a seismic analysis method for railway bridge based on seismic risk assessment was established. Taking a typical 32 m prestressed concrete simply supported beam bridge in the nine-degree seismic region of Chongqing-Kunming high-speed railway line as the research object, five combined seismic isolation systems were compared and comprehensively evaluated by using the seismic analysis method based on seismic risk assessment. The results show that the seismic risk probabilities of piers and bearings can be controlled within 6% and 3% when the seismic isolation system composed of double spherical aseismic bearings, tenon-shaped metal energy dissipation devices and steel anti-drop-beam devices was used. This system can effectively improve the seismic performance of piers, dissipate the seismic energy, reduce the seismic force of pile foundations, and limit the displacement of main girders, then preventing girder falling and realizing the seismic design of 32 m high-speed railway simply supported bridge in nine-degree regions. It provides a basis for seismic analysis of similar bridges in high intensity seismic regions in the future.