A seismic isolation system is designed to reduce the seismic responses of a building, and it has been applied to more and more super-tall buildings. However, for those seismically isolated super-tall buildings in the design for wind, large and long-duration wind loads may cause large wind-induced responses of the buildings, leading to the residual deformation in the seismic isolation layer. Therefore, by analyzing a multi-degree-of-freedom model via typhoon simulation, this paper investigates the maximum wind-induced responses and the residual deformation. Furthermore, the authors clarify how the wind speed and wind direction influence the above analytical results.