This study develops the train sub-model by multibody dynamic theory and establishes the longitudinally connected ballastless track-bridge sub-model using finite element theory. The two sub-models are assembled into a joint simulation model of train–track–bridge system coupling dynamic (JSTTBS) through wheel–rail contact relationships. Then, the influence of interlayer connection failure and pier settlement on the dynamic index of train–track–bridge system is analyzed, the intrinsic topological relationship (ITR) between pier settlement amplitude and dynamic index considering interlayer connection failure is proved, and the pier settlement threshold is proposed. The results showed that the calculation results of JSTTBS considering the interlayer connection failure and pier settlement are in good agreement with the literature data, verifying the model’s accuracy. The void beneath the slab caused by the pier settlement aggravates the train dynamic index change. After considering the void beneath the slab, the maximum value of each dynamic index is about two times that without accounting for the void. The uneven settlement value of the pier derived from the ITR is within 22.47[Formula: see text]mm, which is in good agreement with the calculation result of the established JSTTBS of 23.08[Formula: see text]mm, indicating the reliability of the ITR to calculate the uneven settlement threshold of the pier.
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