The invention relates to a soil heavy metal element content predicting method based on a terahertz spectrum and a deep automatic encoder. Compared with the prior art, the method overcomes the shortcoming that ingredients of soil cannot be comprehensively analyzed and generalized on a large scale. The method comprises the following steps: acquiring and pretreating a soil sample; construction of a predicting model based on the deep automatic encoder: stacking a denoising automatic encoder and a compression encoder on construction of a model to form the predicting model of the deep automatic encoder; training of the predicting model of the deep automatic encoder: inputting terahertz spectrum data for training a sample into the predicting model of the deep automatic encoder to finish training of the predicting model of the deep automatic encoder; and predicting the heavy metal element content of soil. By a structural model of the deep automatic encoder and the terahertz spectrum, ingredients of the heavy metal elements of the soil are analyzed and predicted.