Using the FE-SEA mixed method, this study establishes a coupled model of the 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 subway vibrations. The mechanism underlying the generation of vibrations in overlying buildings is revealed, while also delving into the propagation patterns 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 its natural frequency, with main-frequency vibrations located in the low-frequency band between 31.5 and 50 Hz. 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 the 20~80 Hz range, with A-levels decreasing then increasing as floors rise; application of a vibration isolation support effectively reduces natural frequencies while reducing higher-frequency responses from roof structures above this range. These findings provide a useful reference for predicting, reducing, or isolating subway-depot-related vibrations.