The Dujiangyan–Siguniangshan mountain rack railway project is China’s first mountain rail transit. Most of its lines are located in mountainous areas and close to natural ecological protection areas, which have strict restrictions on the vibration and noise of train operation. At the same time, the vibration of mountain rack railway trains is also an important factor affecting the safety and riding comfort of trains. However, due to the multi-source vibration of gear teeth, wheels, rails, and suspensions, it is difficult to clearly define the vibration characteristics and vibration transmission path of the train, which has a serious impact on its vibration noise suppression and optimization. To this end, this study proposed a set of evaluation methods for the vibration characteristics and transfer paths of mountain rack trains based on a combination of dynamics and operational transfer path analysis (OTPA). Considering the interaction between the dynamic behaviors of the primary and secondary suspensions, the gear tooth contact behavior, the wheel–rail contact behavior and the dynamic behaviors of the track system, a dynamic model of a mountain rack train based on the finite element method was established, and the effectiveness of the model was verified through field experiments. On this basis, the OTPA method was used to establish a vibration transfer path model between the secondary suspension and the center of mass of the car body, and it was used to analyze the vibration mechanism and transfer path of the train body at the rated speed (20 km/h) and the limited speed (30 km/h). This study is of great significance for suppressing the vibration noise of mountain rack trains, reducing the impact on the ecological environment and improving ride comfort.