A three-dimensional seismic wave speed model in the Kanto region of Japan was developed using adjoint tomography for application in the effective reproduction of observed waveforms. Starting with a model based on previous travel time tomographic results, we inverted the waveforms obtained at seismic broadband stations from 140 local earthquakes in the Kanto region to obtain the P- and S-wave speeds Vp and Vs. Additionally, all centroid times of the source solutions were determined before the structural inversion. The synthetic displacements were calculated using the spectral-element method (SEM) in which the Kanto region was parameterized using 16 million grid points. The model parameters Vp and Vs were updated iteratively by Newton’s method using the misfit and Hessian kernels until the misfit between the observed and synthetic waveforms was minimized. Computations of the forward and adjoint simulations were conducted on the K computer in Japan. The optimized SEM code required a total of 6720 simulations using approximately 62,000 node hours to obtain the final model after 16 iterations. The proposed model reveals several anomalous areas with extremely low-Vs values in comparison with those of the initial model. These anomalies were found to correspond to geological features, earthquake sources, and volcanic regions with good data coverage and resolution. The synthetic waveforms obtained using the newly proposed model for the selected earthquakes showed better fit than the initial model to the observed waveforms in different period ranges within 5–30 s. This result indicates that the model can accurately predict actual waveforms.