The investigation of the influence of soil-structure coupling on the vibration propagation pattern is the key to ensuring the reliability of the prediction of train-induced building vibration. This study selects different metro depots with over-track buildings as the research objects based on the existing engineering examples. It analyzes the general laws of vibration propagation from the ground soil to the building columns. The study provides valuable references for predicting vibration and designing vibration isolation measures for over-track buildings. Additionally, this study proposes a vibration prediction method for over-track buildings above metro depots based on the back propagation (BP) neural network model in machine learning. This model considers the soil-structure coupling loss in a data-driven manner based on the rich data samples, which avoids the problems of complex numerical simulation calculations and parameter uncertainties to some extent. This prediction method has a good balance of efficiency and convenience and also meets the accuracy requirements. It was judged to be a promising prediction method for the preliminary design stage of the over-track buildings above metro depots.