The present application provides a method and system for dynamically predicting a deoxynivalenol content of wheat at harvest, including: on the basis of historical data, screening out by particle swarm optimization algorithm combined factors suitable for establishing a prediction model, and establishing the prediction model by using the combined factors; on the basis of data of a current year, predicting a second flowering date and a second harvest date of wheat in the current year by an agricultural model; then obtaining a weather forecast on the basis of the second flowering date and the second harvest date, and combining the weather forecast and geographic data into correlated factors; and finally predicting the deoxynivalenol content of wheat at harvest by means of the prediction model and the correlated factors. Compared with the prior art, statistical items in the prediction model are more comprehensive, and growth period data of the current year can be dynamically predicted on the basis of growth period indexes model, thus continuously adjusting and establishing the prediction model. In addition, an overhead time for screening multi-dimensional large-batch data by the particle swarm optimization algorithm has more advantages, and the prediction model established by a multiple linear regression algorithm has higher precision.