The settlement values of subway tunnels during the construction period exhibit significant nonlinear and spatial–temporal variation characteristics. To overcome the problems of historical data interference and spatiotemporal characteristics in tunnel settlement prediction models, this paper proposes a tunnel settlement prediction method based on data decomposition, reconstruction, and optimization. First, the original data are optimized via the SSA, which has global optimization capability, high noise immunity, and high adaptivity. The original signal is subsequently decomposed into multiple subsignal sequences via a variational modal decomposition (VMD) algorithm combined with a rolling decomposition technique. Finally, the decomposed signals are fed into the machine learning model to construct a high-precision settlement prediction model based on rolling decomposition. The prediction accuracy of different models was analyzed via the measured settlement data during the construction period of the Beijing subway as an example. The results show that the prediction model with the integrated decomposition algorithm reduces the RMSE and MAE by 33% and 37%, respectively, which significantly improves the prediction accuracy and generalization ability of the neural network to meet the demand of practical engineering prediction and simultaneously enhances the risk warning ability of the model.