China railway track system II (CRTS-II) slab ballastless track is usually constructed on high-speed railway (HSR) bridges to ensure the rail smoothness and the running safety of high-speed trains, but the use of the longitudinal continuous track system would significantly alter the dynamic characteristics of the bridges and therefore influence the bridge seismic responses. The pounding at shear keys has also been identified as one of the critical factors affecting the seismic behavior of bridges. To investigate the effects of shear keys and CRTS-II track system on the seismic behavior of HSR simply-supported bridges subjected to transverse earthquake excitations, detailed 3D finite element models are developed by using ABAQUS. The seismic responses calculated from the bridges with and without considering shear keys are firstly compared. The result shows that the shear keys can effectively limit the development of pier-girder relative displacement and thus decrease the potential of girder dislocation. However, large pounding forces would be generated between the shear keys and bearing pads and transferred to bridge piers, which will amplify the seismic responses of the bridge piers. The result of seismic analyses of multiple-span simply-supported bridges with and without considering the track system shows that the track system will significantly influence the distribution of seismic forces among the bridge spans. For a bridge with equal pier heights, considering the track system will reduce the seismic responses of side spans (close to subgrade) but will increase those of the middle spans. Whereas an opposite trend is found for bridges with high middle piers and short side piers.