Many significant geological features in central Japan reflect the history of tectonic events such as volcanic eruptions, fault ruptures, and the collision of the Izu‐Bonin arc. Because most previous studies focused on deep, large‐scale structures at relatively low resolution or on local structures using high‐resolution data (e.g., active source seismic data), tectonic structures over a wide area throughout central Japan have not been characterized in detail. In this study, we estimated 3D S wave velocity structures with high spatial resolution by extracting surface waves from 1‐year‐long ambient seismic data recorded by the Hi‐net high‐sensitivity seismograph network. We computed cross spectra of ambient noise data between station pairs and then extracted phase velocity dispersion curves using a frequency domain method. We developed an algorithm to calculate phase velocity and obtained numerous dispersion data. We then estimated the 3D S wave velocity structure by applying a direct surface‐wave inversion method. Our results clearly mapped heterogeneous features such as tectonic lines, sedimentary plains, and volcanic systems. We observed some low‐velocity anomalies below volcanoes. Active fault zones identified as low‐velocity zones were consistent with features on seismic reflection profiles. Several geological blocks that are related to the Izu collision were observed around the Izu Peninsula. We observed previously unreported geological features of the island of Honshu. Our high‐resolution S wave velocity model can be used for not only interpretation of geological structures but also hazard assessment of earthquake.