Characterized Green’s function method (CGFM), a new approach for estimating the response spectra of earthquake ground motion, has been proposed by Oji et al. (2012). The CGFM is based on the concept that the spatial average of estimated results is equal to a conventional attenuation model. The site‐specific deviations can be modeled by the source rupture effects, such as directivity pulses and radiation patterns, which are represented by the frequency‐dependent factors obtained from a superposition of simple characterized waveforms obeying the omega‐square model. In this article, we expand the CGFM to include nonlinear site response at a specific site. This response is calculated using the estimated time history of ground motion on the engineering basement from the response spectrum and the simulated phase waveform obtained by the original CGFM. The proposed CGFM is verified by comparing the estimated results with the records from the 1995 Kobe and the 2007 Chuetsu‐Oki earthquakes, Japan.