Track–bridge interaction under the seismic excitation is a dominant factor to the design and operation of railway bridges. A spatial model integrating rails, deck system, stringers, cross beams, suspenders, main trusses, piers and foundations was established in this paper, adopting non-linear springs to simulate the longitudinal resistance between the track and the bridge. The improved Penzien model was utilised to simulate the soil-pile interaction effect and a computer program was developed to generate artificial seismic waves. Comparison of natural vibration characteristics for the track–bridge system with and without considering the track constraint was made. Furthermore, the effects of sensitive parameters were investigated, including the ballast resistance, friction of movable bearings, location of rail expansion joint (REJ), etc. Present study results indicate that the track–bridge interaction enhances the structural integrity and induces relatively higher natural frequencies of the bridge. In general, the response obtained by the ballast resistance specified in the Chinese code is smaller than that by UIC code. Neglecting the friction of movable bearing will lead to over-estimated rail stresses and under-estimated internal forces of some piers in the system. Setting REJ at both beam ends is more efficient to release the seismic stress of the rail on the bridge.