To maximize the use of urban land, many cities have built buildings above metro depots. However, the low-frequency vibration caused by metro operation affects the lives of surrounding residents, which seriously restricts the further development of over-track buildings. To study this problem, Firstly, the vibration of the metro depot and surrounding sensitive areas are tested on a large actual metro depot in Southwest China, and the rail, sleeper/support column, bearing column, and cover plate are mainly tested. Then, considering nonlinear factors such as mechanical properties of building materials, soil layering characteristics, and artificial viscoelastic boundary, the numerical coupled model of the train-track-depot-building is established, and the simulation data are compared with the test data to verify the accuracy of the numerical model. Finally, the impact of metro operation on the over-track buildings is evaluated. Results show that for the over-track buildings concerned in this paper, the floor vibration near the rail is the strongest, the main vibration frequency of the office building is concentrated in 10–20 Hz, and the maximum Z vibration level (VLzmax) of the office building is 52.02 dB. The main vibration frequency of the residential building is similar to that of the office building, and the superposition of floor vibration energy causes the vibration of the mid-span point to be larger than the vibration of the corner point and the side wall point. The vibration wave of lower floors mainly propagates through the bearing column, and the vibration of the parking garage is larger than other buildings. The research results can provide a reference for the vibration control and design of over-track buildings above the metro depot.@en