This paper presents a study of the dynamic behavior of freight train-track-bridge system during a heavy haul train crossing a bridge from normal operation condition to derailed state due to a severe track defect. A coupled Finite Element–Multibody dynamics (FEMBS) model including the freight train sub-model, the ballast track sub-model, the contact sub-models and the bridge deck sub-system is formulated. This model is capable of predicting the normal operation, derailment/post-derailment behavior of a freight train running on tracks supported by bridge and embankment, as well as the dynamic response of track structures and bridge under train passage. The effects of the wavelengths of track defects on the running safety of freight trains running on bridge and embankment are reported. The results show that severe track defects can arouse the resonance of the train-track-bridge system, and the safety limits for track defects on bridge should be stricter than that on embankment.