The work aims to study the dynamic characteristics of a spacecraft during transportation and the influence of the adapter material on its vibration characteristics. With the spacecraft-adapter-transport cylinder system as the study object, the flexible multi-body dynamic model was established by the ABAQUS finite element software. The modal analysis and harmonic response analysis of the model were carried out. The first four-order mode shape of the system and the displacement response curve of the key nodes of the spacecraft were obtained. Finally, the elastic modulus, damping and the influence of the thickness ratio of the adapter sponge and polyurethane foam on the vibration displacement of the spacecraft were analyzed. The high-order inherent frequency of the spacecraft and transport cylinder had little impact on the dynamic performance of the spacecraft structure. The harmonic response vibration displacement of its head was the largest, and the displacement was reduced with the increase in the elastic modulus and damping of the adapter’s polyurethane foam. The damping performance was the best when the thickness ratio was approximate to 7∶40. Such method can provide the basis for the selection of the material characteristics of the adapter and the design of the structural parameters accurately and effectively.