The power of passive ventilation cooling of spent fuel is based on the natural circulation generated by the difference in air density. In this process, the temperature difference between the storage area and the external environment will affect the passive ventilation and cooling of the spent fuel. On this basis, the effect of storage area height on passive cooling of spent fuel is studied. Through numerical simulation, the influence law of the height of the heat storage area is obtained, and the natural cycle cooling capacity of the spent fuel storage unit is effectively increased. The design parameters of the scheme remain unchanged, and only the height of the storage area is changed for simulation calculation. In the simulation results, the temperature of the spent fuel storage vessel is selected as the evaluation parameter. By changing the bottom of the storage area, the distance between the upper end of the spent fuel storage container and the ceiling of the storage area is different, and the height of the storage area is changed. The simulation results show that the greater the distance between the upper end of the spent fuel storage container and the roof of the storage area, the lower the maximum temperature and average value of the spent fuel storage container, that is, the better the heat dissipation effect. In the workshop design, under the condition of considering other economic factors, the distance between the upper end of the spent fuel storage container and the ceiling of the storage area should be increased as much as possible to achieve the best heat dissipation effect.