With the continuous increasing of national reserves, column-supported group silo structures are widely used. However, the seismic performance of group silos is more complex than that of single silo due to multiple adverse factors such as and uneven vertical stiffness distribution. Therefore, this study is focused on a practical grain column-supported silos to study the dynamic characteristics of silo structures. Firstly, the refined numerical simulation model of the silo was verified by comparing with shaking table test. In addition, the interaction mechanism of the storage structure in Abaqus finite element software were also explored. Finally, numerical simulation models were established for three different silo structural systems, namely single silo, row silo, and group silo. The dynamic characteristics of vibration modes and natural frequencies of different structural systems were compared comprehensively. The results show that the single and row silos mainly exhibit horizontal torsional modes, with the lower supporting columns as the main deformation region, which demonstrates the vulnerability of the lower part in the actual engineering. Moreover, the vibration pattern of the group silo is similar to that of the single and row silos, but the overall torsional effect is stronger. The structure is characterized by “upper rigid and lower flexible”. When the mass of stored material is increased, the frequency is decreased in silo structures.