A three-dimensional rail-bridge coupling element of unequal lengths in which the length of the rail element is shorter than that of the bridge element is presented in this paper to investigate the spatial dynamic responses of a train-track-bridge interaction system. Formulation of stiffness and damping matrices for the fastener, ballast, and bearing, as well as the three-dimensional equations of motion in matrix form for a train-track-bridge interaction system using the proposed element are derived in detail using the energy principle. The accuracy of the proposed three-dimensional rail-bridge coupling element is verified using the existing twodimensional element. Three examples of a seven-span continuous beam bridge are shown: the first investigates the influence of the efficiency and accuracy of the lengths of the rail and bridge elements on the spatial dynamic responses of the train-track-bridge interaction system, and the other two illustrate the influence of two types of track models and two types of wheel-rail interaction models on the dynamic responses of the system. Results show that (1) the proposed rail-bridge coupling element is not only able to help conserve calculation time, but it also gives satisfactory results when investigating the spatial dynamic responses of a train-trackbridge interaction system; (2) the double-layer track model is more accurate in comparison with the single-layer track model, particularly in relation to vibrations of bridge and rail; and (3) the no-jump wheel-rail interaction model is generally reliable and efficient in predicting the dynamic responses of a train-trackbridge interaction system.