The construction of 3-D basin velocity structures is ongoing in many regions of Japan. The structure models are constructed mainly for the prediction of long-period ground motions from future large earthquakes. In this paper, we validate the 3-D velocity structure model of the Tokachi basin, a deep sedimentary basin located in eastern Hokkaido, Japan, based on 3-D simulation of long-period (2–20 s) ground motions from three nearby intermediate-depth earthquakes; this model was constructed by the National Research Institute for Earth Science and Disaster Prevention (NIED). We make comparisons between the observed and synthetic long-period ground motions for the basin-induced surface waves as well as the direct S-wave. We also try to revise the 3-D velocity structure in the western part of the Tokachi basin based on 1-D velocity structures estimated using long-period S-wave modeling and the microtremor survey method. We then perform the 3-D simulation again to validate the revised model. Based on quantitative comparisons of the long-period ground motions from these simulations with those observed, we conclude that the NIED and revised velocity structure models are generally good at the central basin sites, but that both models require modification at the basin edges to explain the details of the observed basin-induced surface waves.