An isolated building, composed of superstructure and isolation system which have very different damping properties, is typically non-classical damping system. This results in inapplicability of traditional response spectrum method for isolated buildings. A multidimensional response spectrum method based on complex mode superposition is herein introduced, which properly takes into account the non-classical damping feature in the structure and a new method is developed to estimate velocity spectra from the commonly used displacement or pseudo-acceleration spectra based on random vibration theory. The error of forced decoupling method, an approximated approach, is discussed in the viewpoint of energy transfer. From the baseisolated benchmark model, as a numerical example, application of the procedure is illustrated companying with comparison study of time-history method, forced decoupling method and the proposed method. The results show that the proposed method is valid, while forced decoupling approach can\'t reflect the characteristics of isolated buildings and may lead to insecurity of structures.