As a sustainable mode of metro-development strategy, transit-oriented development (TOD) is rapidly growing to finance the transport infrastructure investment. The main negative consequence of constructing residential buildings directly over metro depots is railway-induced vibration, that may affect structural serviceability. The residents may feel uncomfortable, as the metro trains start running very early in the morning and finish daily operations very late at night. In order to evaluate the level of human comfort subject to the special situation, a case study was provided in this paper. Directed by the academic review, there were four common comfort evaluation methods, with difference indexes to describe the influence of vibrations. Therefore, a measurement campaign was conducted and both acceleration and velocity sensors were simultaneously installed at the same measurement points, to reduce the influence of the conversion accuracy. The results show that there are certain differences between the evaluation methods in assessing the vibration comfort, but considering the most adverse effects together, the over-track building at this particular TOD-developed depot can ensure that 90% of the occupants would not be highly annoyed by the vibrations. The main negative effect on human comfort at the TOD depot is that the high-level vibrations would cause interruptions in sleep. Among them, the vibrations in this case would affect the rest of 17% of the occupants in the bedrooms on the seventh floor, and make it difficult for 9% of the occupants to fall asleep. Therefore, the evaluation index was suggested to consider more factors related to sleep difficulties and awake threshold values.