When constructed on tall building rooftops, the vertical axis wind turbine (VAWT) has the potential of power generation in highly urbanized areas. In this paper, the ambient dynamic responses of a rooftop VAWT were investigated. The dynamic analysis was based on ambient measurements of the structural vibration of the VAWT (including the supporting structure), which resides on the top of a 24-story building. To help process the ambient vibration data, an automated algorithm based on stochastic subspace identification (SSI) with a fast clustering procedure was developed. The algorithm was applied to the vibration data for mode identification, and the results indicate interesting modal responses that may be affected by the building vibration, which have significant implications for the condition monitoring strategy for the VAWT. The environmental effects on the ambient vibration data were also investigated. It was found that the blade rotation speed contributes the most to the vibration responses.