The settlement in the transition zone between track and bridge has been a big problem to railway operation. As the higher speed and axle-load wagons are continuously demanded by rail heavy-haul industries in Australia, it has been observed that the higher speed and axle-load traffic has led to many problems associated with the track-bridge transition zone, which could be mainly categorized into three aspects: rapid track geometry degradation, ballast mud pumping, and track component plastic deformations, forming transition zone settlement. The settlement is mainly due to the sudden change of railway substructure supporting conditions and unavoidably excites the dynamic interactions of vehicle-track-bridge, causing more frequent damages to their structures, including increased wear and rolling contact fatigue defects, even train derailment, and possible higher capital costs to the maintenances. However, the attention has been paid to evaluate the abilities of existing track-bridge transition zone structures to accommodate the higher speed and axle-loads and to improve the transition zone design. In the investigations on the dynamic behaviours in a track-bridge transition zone in a heavy-haul network, a detailed rail track-bridge model and vehicle models are developed by using Gensys multi-body dynamics software. The rail and bridge structures are considered as the finite Euler–Bernoulli beam elements, and the vehicles are modelled by using multi-body dynamics approach. The dynamic behaviours are simulated due to the train travelling across the track-bridge transition zone with and without settlements, and the effect of operation speeds and track settlement dip defects in the transition zone on the wheel-rail dynamic load can be further understood, and the effect of various bridge transition zone designs and critical parameters can be examined.