The deformation of bridge structures will cause deterioration of geometry on the rail surface during the service period, which will threaten the normal operation of train. A train–track–bridge coupling dynamics model was established. In order to simulate real operational conditions, initial geometric irregularity was taken into account, which was combined with rail irregularity caused by different vertical deformation of girder and was superimposed as external excitation. The probabilistic and statistical characteristics of operational performance indexes were analysed. The sensitivity of operational performance indexes to different deformation modes was studied. The vertical deformation thresholds of girder based on probability guarantee rate were obtained. The results show that unloading rate of wheel and wheel/track vertical force are more sensitive to single vertical rotation deformation mode. Vertical acceleration of the train and sperling index are more sensitive to bilateral vertical rotation deformation mode. Unloading rate of wheel is more sensitive to single vertical translation deformation mode. In the process of enhancing daily operation, single vertical rotation and multiple vertical translation should receive significant attention.