In this paper, we simulated frequency responses of subsurface due to incident SH wave by using discrete wave number method (DWM: Aki-Larner Method). It is useful in constructing the models of the non-uniform subsurface. We estimated subsurface profile based on the resonance frequency of HVSR method comparing with frequency responses obtained from SH waves incident by DWM. The only information from HVSR is the resonance-frequency of the ground. Although what obtained from the numerical analysis by DWM is a response function, it coincides with the response of the surface ground if the input motion is a white noise and the ground behaviour is a liner. In this case, the peak of response function can be considered to be a resonance frequency of the ground. Therefore, we here compared the peak frequencies of HVSR curve and response functions. To estimate the resonance frequency of ground by HVSR, the single observations of microtremor at 161 sites were carried out by using the three-component accelerometer with a data logger, GPL-6A3P, in the study area of Ende Regency that is one of five regencies in East Nusa Tenggara Province on the island of Flores, Indonesia. The results show that site response in Ende area varies the resonance frequencies span 0.7-1.4 Hz. For DWM, we assume simple two layered media with irregular boundary aimed at making a simple ground profile of the study area. The two-layered model is composed of a ‘soft basin’ on engineering bedrock. We varied the depth and the shear wave velocity of the basin and calculated response functions by using DWM. Then we selected the best fit parameters by comparing the resonance frequency of H/V result. Finally, we proposed a possible non-uniform ground model in the study area.