The Yufutsu Plain, a sedimentary basin surrounded by mountains, is located in the southern part of the Ishikari-Yufutsu Lowlands, Hokkaido, Japan. The Hidaka arc-arc collision zone, located in the eastern part of the Yufutsu Plain, forms the Hidaka Mountain range in central Hokkaido, with the Ishikari-Teichi-Toen Fault Zone of the Ishikari-Yufutsu Lowlands on the west side, which forms part of a major geological boundary that extends in the north-south direction. The 2018 Hokkaido Eastern Iburi earthquake (Mw 6.6) occurred at 03:08 JST on September 6, 2018, in this arc-arc collision zone. The K-NET HKD126 station in Mukawa Town, which is close to the severely damaged basin margin area, recorded strong-motion data with strong power for a period of 1–2 s during the main shock. The site amplification characteristics of the shallow S-wave velocity structure, which was estimated from microtremor array observations and surface wave explorations, were one of the causes of this strong ground motion. It is essential to accurately estimate the depth of the seismic bedrock and basin margin to evaluate the long period of large earthquakes. In this study, we used strong-motion data recorded at HKD126 and three temporary strong-motion stations near the basin margin area to tune the deep S-wave velocity structure. First, we performed microtremor array observations and surface wave explorations to estimate the S-wave velocity structure to a depth of 1 km beneath the station at the hill site because a detailed shallow structure is not available for this site. Then, with a combination of the estimated S-wave velocity structure and the existing structure, we tuned the deep structures based on an autocorrelation function analysis using strong-motion data. The validity of the estimated structures from the shallowest depth to the seismic bedrock was verified based on the observed arrival time and theoretical travel time differences for the S-wave initial motion. We estimated the seismic bedrock of the four stations to be at a depth of 7–10 km. In addition, an autocorrelation function analysis suggests topological basement irregularity.