Abstract: In the process of service, bridge misalignment phenomenon will inevitably occur in the rack-rail railway, which leads to abnormal deformation of the rack rail, and then to the local stress of the rack rail and connecting parts surge, and it is very likely to damage the structure of the rack rail, and ultimately a serious threat to the safety and stability of the vehicle operation. In this study, we construct a nonlinear dynamic interaction model for a vehicle-rackrail (rail)-bridge system under bridge misalignment, study the deformation, stress, acceleration and connection bolt stress change rule of the rail when the vehicle passes through the bridge with large gradient under misalignment phenomenon, and put forward the safety control threshold of bridge misalignment on the basis of this. The results show that: under the combined effect of multiple loads such as gear rack rail meshing action and wheel-rail action, the misalignment phenomenon is very likely to lead to fracture of rack rail connecting bolts. For the research parameters of this study, the maximum deformation of the rack rail at the mid-span position of the bridge reaches 11.15 mm; when the amount of misalignment is 7.07 mm, the bolt reaches its permissible shear strength; and the misalignment of the bridge does not have much influence on the vibration and on the stress of the rack rail. The study results can be used to provide a theoretical basis for the pre-design and post operation and maintenance of rack railway.