Adjoint waveform tomography, which is an emerging seismic imaging method for the crust-and global-scale problems, has gained popularity in the past and present decade. This study, for first time, applies adjoint waveform tomography to the large volume of seismic data recorded by the densely spaced, permanent monitoring network that covers the entirety of Japan. We develop a heterogeneous shear-wave velocity model of central Japan that agrees with the geology and lithology. The results reduce the time-frequency phase misfit by 16.2% in the 0.033–0.1 Hz frequency band and 3.6% in the 0.033–0.125 Hz band, respectively. We infer that some velocity anomalies resolved in this work reflect the volcanic fluids, thick sedimentary basins, and granitic rocks. The results of this study suggest the possibility of imaging heterogeneous subsurface structures around Japan island using waveform tomography with a densely distributed network of permanent seismometers.