The observation of foundation settlement of substation equipment has been researched and applied, but the prediction of substation equipment foundation settlement has not yet been reported. In this paper, through the regular observation of equipment foundation settlement, we constructed a prediction method based on the frequency domain decomposition of FEDformer model in the equipment foundation settlement, and the experimental results show that, compared with the other models in the long time series prediction problem, FEDformer has been greatly improved in the computational efficiency and prediction accuracy, and it can be used to make effective prediction of the foundation settlement of substation equipment.