Abstract: Granular grain building warehouse has been the new type of grain storage warehouse in recent years. The grain warehouse and vertical grain silo can be integrated to fully utilize the space for the land saving, particularly suitable for the requirements of low-carbon environmental protection and sustainable development. Among them, the seismic performance of the structure can dominate the dynamic characteristics of the granular grain building warehouse under different storage conditions. However, the previous data of silo cannot be directly applied to the dynamic characteristics of granular grain building warehouse under different storage conditions. Therefore, this study aims to explore the dynamic characteristics of a granular grain building under different storage conditions. Specifically, a 1/25 scale Plexiglass model was designed (The model was three floors, each containing a interlayer) to combine with an actual granular grain storage warehouse. The overall distribution was also considered for the empty and the full warehouse state with the stored material at different heights. The shaking table modal tests were carried out using the ABAQUS finite element (FE) analysis and the theoretical calculations of the natural frequency. In addition, three natural frequencies were then compared after simulation. The results show that the storage quality of granular grain building warehouse posed the significant influence on the dynamic characteristics of the structure. When the storage material was only stored on the first floor, the natural frequency of the structure was reduced by 1.20%, compared with the empty warehouse condition, indicating the small difference. Once the storage quality was accumulated from one to three layers, the natural frequency of the structure was reduced by about 33% for the granular grain storage warehouse structure, as each layer was accumulated. Meanwhile, there was a significant impact of the distribution position in the granular grain building warehouse on the dynamic characteristics of the structure. When the storage quality was constant (single-layer full warehouse), the natural frequency of the granular grain building warehouse structure decreased by about 35%, as the storage position increased by one layer. The material storage shook more outstandingly, when the storage material was in a higher position. As such, the damping ratio of the structure increased gradually, as the position of material storage increased, indicating the more significant effect of shock absorption and energy consumption of the material storage. Furthermore, the feasible FE model of granular grain building warehouse was selected from the reasonable numerical simulation for the structural dynamic response analysis in the subsequent step. Anyway, the storage (single full storehouse) was greatly contributed to the interlayer stiffness and quality of the grain storage warehouse structure. The inter-story stiffness contribution coefficient of each storage layer to that layer was 1.16, and the mass distribution coefficients of the storage material to the upper and lower mass points were 0.13 and 0.87, respectively. Consequently, the strong reference was offered for the accurate calculation of stiffness contribution coefficient and mass distribution coefficient. The finding can also provide a theoretical reference for the dynamic response analysis and seismic design of granular grain building warehouse.