Abstract: When subjected to earthquake motions, the deep soft soil easily undergoes large deform due to its low shear modulus. The equivalent linear method is traditionally used to perform site response. For deep soft deposit site, the high frequency composites and peak acceleration values of the site response are underestimated if the equivalent linear method is used. It is dangerous for the structure if the site response is used to perform anti-seismic design. The frequency-dependent equivalent linear method is proposed in this paper. It considers the moving average and Parzen spectrum window theory. Results of the two methods are compared with the observed earthquake motions. This comparison shows that the method proposed in this paper is more effective than the traditional method in simulating wave propagation in the deep soft site. Finally, the two methods are used to perform the site reponse for one engineering site located at Binhai New District. The results are analyzed.