To investigate the effects of different storage temperatures humidity, and processing methods on the contamination levels of four types of Alternaria toxins (AME, AOH, TeA, TEN) in wheat grains, as well as their variations, providing a scientific basis for the safety risk control across the entire wheat and wheat product industry chain. Methods Positive samples were obtained from random sampling in a province for storage experiments and subsequently processed into steamed buns, noodles and bread. The contamination levels of the four types of Alternaria toxins were determined before and after the storage process and processing, and the effects of storage and processing on toxin residues were assessed by the processing factor. Results During the 12-month storage period, the content of the four types of Alternaria toxins in wheat showed a trend of first decreasing and then stabilizing. However, the storage duration had no significant effect on contamination levels (P > 0.05). The average processing factors for AME, AOH, TeA, and TEN was 0.77, 0.61, 0.51, and 0.73, respectively. There was no statistically significant difference in the effect of temperature and humidity on toxin contamination levels during storage (P > 0.05). The impact of different processing methods on the contamination levels of the four mycotoxins also showed no significant difference (P > 0.05), and the average processing factors for contamination levels in wheat products were less than 1. Conclusion Alternaria toxins contamination level was limited by temperature and humidity under standardized storage conditions, and the Alternaria toxins levels showed a trend of first decrease and then stabilization within 12 months. Meanwhile, processing wheat into products effectively reduced the contamination level of Alternaria toxins. The processing factor provide a quantitative basis for evaluating the detoxification or reduction effects of different processing techniques and can provide a reference for risk assessment of Alternaria toxins.