We perform three-dimensional (3D) finite-difference (FD) waveform modeling of strong motions in the frequency range 0.2 to 1.67 Hz observed in the Sendai basin, Japan, during the Japan Meteorological Agency magnitude (MJ) 5.0 1998 Miyagiken-Nanbu earthquake. In a previous, we estimated S-wave velocity structures above the pre-Tertiary bedrock at six sites in the Sendai basin based on array records of microtremors. To interpolate these velocity structures in space we conduct single-station microtremor measurements at a total of 61 locations and estimate the S-wave velocity structure at each site by modeling the horizontal-to-vertical spectral ratio of fundamental mode Rayleigh waves. An initial 3D model of the basin is constructed using the velocity structures estimated from both array and single-station microtremor measurements, along with other information such as surface geology. This model encompasses a region 33 km long, 30 km wide, and 19 km deep. The final model is obtained through a trial-and-error process by fitting 3D FD synthetic waveforms to the bandpass-filtered (0.2 Hz to 1.67 Hz) displacement records 12 stations for the 1998 Miyagiken-Nanbu earthquake. We compute the synthetics using a fourth-order staggered-grid 3D FD method with variable grid spacing. As the 3D model is modified, the source parameters (strike, dip, rake, and seismic moment) are estimated by a grid search method using 1D site-specific models derived from the modified 3D model. The observed waveforms are reproduced well at most stations by the final 3D basin model. This agreement suggests the validity of the final 3D basin model for theoretical strong-motion prediction of large earthquakes in the frequency range from 0.2 to 1.67 Hz.