With the gradual use of packaging boxes for potato storage, the influence of different stacking methods on the storage effect of potatoes was studied. This study used direct computational fluid dynamics numerical methods to simulate the models of potatoes in packaging boxes under different stacking forms. By comparing and analyzing the gas velocity and temperature distribution uniformity in various stacking forms, the impact on the storage effect was analyzed, and the optimal stacking method was determined. The results showed that the gas velocity in the intermediate layer of the packaging box was relatively high, resulting in a lower temperature of the potatoes. The gas velocity in the other planes was lower, and the temperature of the potatoes was higher than that in the intermediate layer but with a more uniform distribution. After 300 minutes of ventilation, the temperature of the potatoes in the packaging box decreased to 3~5 ℃, meeting the expected requirements and demonstrating good ventilation effects. For different stacking patterns, when arranged in a staggered pattern, the maximum gas flow velocity on the upper and lower planes was 2.5 times the minimum value, and the maximum temperature difference was 0.2 °C. On the middle plane, the maximum gas flow velocity was 4.8 times the minimum value, with a difference of about 2.85 m/s, and the gas flow velocity inside the bin was uniform, with a good cooling effect. For the storage of boxed potatoes, the staggered arrangement stacking method should be prioritized to achieve better storage results.