To conduct practical evaluations of the long-period ground motions (period of 4 to 8 s) in a laterally inhomogeneous large sedimentary basin, we constructed a three-dimensional (3D) sedimentary velocity structure model for the northern Kanto Basin in Japan using a simple velocity gradient function, where strong lateral variations of seismic velocities in the sediments were expected. The model construction employs waveform analysis and geophysical data from vertical seismic profiling and microtremor surveys in the target region. To validate the velocity structure model, we conducted large-scale 3D finite-difference method simulations of the long-period ground motions for two shallow moderate earthquakes: the northern Tochigi earthquake and the northern Ibaraki earthquake. The simulation results for both earthquakes accurately reproduced the observed long-period ground motions in terms of arrival times, amplitudes, and durations of surface waves. By detailed comparisons of the seismograms for observational and simulated data, we demonstrated that the lateral variation of the seismic velocities in the sediments determines the characteristics of the surface wave propagation in the northern Kanto Basin. Such analyses can provide a better understanding of the complex propagation characteristics of surface waves in laterally inhomogeneous, large sedimentary basins.