A new type of grain silo, the semi-underground, double-storey squat silo (SUDSSS) can ensure grain quality and offers the advantage of saving land and energy, besides producing low carbon emission. Numerical simulations were used to analyze the stress and displacement of the SUDSSS under different working conditions during normal operation. The mechanical properties of the upper and lower storeys of the SUDSSS were studied under different static grain storage heights. The results show that an empty silo is the most unfavorable condition and that the underground silo should be prioritized during grain loading, according to the displacement cloud analysis. The stress on the silo wall of the upper storey (above the ground surface) increases as the grain storage height increases, and this stress increases significantly from 1/4 the wall to middle layer. The stress on the underground silo wall of the lower storey (underground) decreases as the grain storage height rises, and the maximum value is reached at the contact point between the wall and the bottom of the silo. The stress on the middle layer is the largest at the center cylinder and on the outer side, and the stress at the bottom of the silo is the largest at 1/3 the distance from the outer side. Our study provides theoretical support and technical guidance for the optimal engineering design of an SUDSSS.