Using the FE-SEA mixed method theory, this study establishes a coupling model of vehicle-track-cover-upper covered building to analyze the impact of subway car depot operation on vibration and indoor secondary structure noise in an upper covered building. The vibration and noise of the roof building and indoor secondary structure in different frequency domains are analyzed under the influence of subway vibrations. The mechanism underlying the generation of vibrations in overlying buildings is unveiled, while also delving into the propagation laws governing vibration and noise in such structures. Results show that the FE-SEA mixed method accurately predicts roof-building vibrations and indoor structural noise. Each floor"s vibration is affected by natural frequency, with main-frequency vibrations located in low-frequency bands between 31.5~50Hz. Vehicle-induced roof-building Z-vibration levels attenuate to their lowest point on the ninth floor before magnifying as floors increase; typical room secondary structure noise pressure mainly concentrates within 20~80Hz ranges, with A-levels decreasing then increasing as floors rise; application of vibration isolation support effectively reduces natural frequencies while reducing higher-frequency responses from roof structures above this range. These findings provide useful reference for predicting, reducing, or isolating subway-depot-related vibrations.