The autocorrelation of ambient noise is used to capture reflected waves for crustal and sedimentary structures. We applied autocorrelation to strong‐motion records to capture the reflected waves from sedimentary layers and used them for tuning the S‐wave velocity structure of these layers. Because a sedimentary‐layered structure is complicated and generates many reflected waves, it is important to identify the boundary layer from which the waves reflected. We used spectral whitening during autocorrelation analysis to capture the reflected waves from the seismic bedrock with an appropriate smoothing band, which controls the wave arrival from the desired layer boundary. The effect of whitening was confirmed by the undulation frequency observed in the transfer function of the sedimentary layers. After careful determination of parameters for spectral whitening, we applied data processing to the strong‐motion records observed at the stations in the Shimousa region of the Kanto Basin, Japan, to estimate the arrival times of the reflected waves. The arrival times of the reflected waves were found to be fast in the northern part of the Shimousa region and slow in the western and southern parts. These arrival times are consistent with those obtained using existing models. Because we observed a slight difference in the arrival times, the autocorrelation function at each station was used for tuning the S‐wave velocity structure model of the sedimentary layers using the inversion technique. The tuned models perfectly match the autocorrelation functions in terms of the arrival time of the reflected waves from the seismic bedrock.