The scientific rationality of farmers’ grain storage technology and equipment is crucial for the biosecurity of grain in the main grain-producing areas represented by Northeast China. In this paper, four farmer grain storage mock silos of different widths were used as a means to track an experimental cycle of grain storage. The absolute water potential of corn in all four silos at the beginning of the experiment was greater than the absolute water potential of air, prompting moisture migration from the grain interior to the air and down to about 14%. Moisture was influenced by wind direction, and moisture decreased faster with better ventilation on both sides of the grain silos. Therefore, grain silo width has a significant effect on the drying effect under naturally ventilated conditions of maize ears. This research focused on the determination and assessment of mycotoxin contamination under farmers’ storage grain conditions and analyzed the effect of silo structure on the distribution of mycotoxin contamination. When the width was too large, areas of high mycotoxin infection existed in the middle of the grain silo, and ventilation and tipping could be used to reduce the risk of toxin production. This study proved that reasonable farmer grain storage techniques and devices in Northeast China can effectively protect grain from mycotoxin contamination.