Based on the mathematical model of internal air flow, heat and humidity coupled transfer in paddy grain piles, while combined with the dynamic model of paddy yellowing, the paper adopted the method of numerical simulation to compare and study the variation of temperature, moisture content and paddy yellowing in the stored grain inside the shallow round warehouse under the conditions of annual natural storage and staged natural storage. On the basis of temperature and humidity, this paper further considered the yellowing effect on the quality of long-term storage of paddy. The results showed that, at the end of storage for 365 days, the average temperature of staged natural storage with ventilation was about 18 ℃ lower than that of natural storage throughout the year, the average moisture was about 0.5% lower, and the average yellowing value was about 0.8 lower. Low temperature air flowling into the high temperature granary could not only reduce the temperature, but also reduce the grain moisture and alleviate the process of paddy yellowing, so the phased natural storage was more conducive to the long-term quality storage of paddy. The rice near the warehouse wall was easily affected by the external ambient temperature, and the coating could be applied on the outside of the warehouse wall to reduce the influence of solar radiation.