We conducted centroid moment tensor (CMT) inversions of moderate ( Mw 4.5–6.5) earthquakes in the Kanto region, Japan, using a local three-dimensional (3D) model. We then investigated the effects of our 3D CMT solutions on long-period ground motion simulations. Grid search CMT inversions were conducted using displacement seismograms for the periods of 25–100 s. By comparing our 3D CMT solutions with those from the local one-dimensional (1D) catalog, we found that our 3D CMT inversion systematically provides magnitudes smaller than those in the 1D catalog. The Mw differences between 3D and 1D catalogs tend to be significant for earthquakes within the oceanic slab. By comparing the ground motion simulations of the 1D and 3D velocity models, we confirmed that the observed Mw differences could be explained by the differences in the rigidity structures around the source regions in the two models. The 3D velocity structures (especially oceanic crust and mantle) are important for estimating seismic moments in intraslab earthquakes. The seismic moments directly affect the amplitudes of ground motions. Thus, 3D CMT solutions are essential for precise forward and inverse modeling of long-period ground motion. We also conducted long-period ground motion simulations using our 3D CMT solutions to evaluate the reproducibility of long-period ground motions at stations within the Kanto Basin. The simulations of our 3D CMT solutions well-reproduced observed ground motions for periods longer than 10 s, even at stations within the Kanto Basin. The reproducibility of simulations using our 3D CMT solutions was better than those based on the solutions in the 1D catalog.