The vibration of the main beam structure of the spent fuel crane and the swing of the payload will affect the safety of the main beam structure and the positioning accuracy of the payload. A multi-body rigid-flexible coupling system dynamics model composed of flexible main girder, trolley and payload is established. The second type of Lagrange equation is used to derive the dynamics differential equations, and the vibration modes of the main beam are solved by the Newmark-β method. The effects of the system's multi-parameters on the vibration characteristics of the main beam and the swing characteristics of the payload are analyzed in simulation. The results show that the increase of the mass of the lifting trolley and the payload significantly affects the vibration amplitude of the main beam and the swing angle of the payload, and the first-order mode of the main beam dominates the vibration process; the running speed of the lifting trolley has no significant effect on the vibration amplitude of the main beam.