As a new type of grain storage structure, the double-story squat silo (DSSS) can ensure the quality of grain storage, but also has the advantages of land saving, energy saving and carbon reduction, and high degree of mechanization. In this paper, the method of coupling discrete elements and finite elements was adopted to construct a mathematical analysis model of the dynamic response between grain particles and the silo wall during the central unloading process in a double-layer shallow round silo (DSSS). The validity of the scaling method was verified by combining experimental tests with the scaling model. Numerical analyses of the scaled-down model were compared with theoretical calculations to confirm the feasibility of the numerical methods, and the grain-silo interaction during the central unloading of the DSSS was investigated. The results showed that both the upper and lower layers exhibited a sudden increase in lateral pressure and oscillation during the unloading process, with a larger overpressure coefficient and a greater tendency for overpressure to occur in the middle of the silo wall. The stresses in both layers of the silo wall reached their maximum at 1/4 of the distance from the bottom of the silo wall when considering the grain-silo interaction. This study has provided technical support for the structural design of DSSS, facilitating its promotion and application, and had significant engineering implications.