Accurately modeling time-dependent coseismic crustal deformation as observed on high-rate Global Navigation Satellite System (HR-GNSS) lends insight into earthquake source processes and improves local earthquake and tsunami early warning algorithms. Currently, timedependent crustal deformation modeling relies most frequently on simplified 1D radially symmetric Earth models. However, for shallow subduction zone earthquakes, even lowfrequency shaking is likely affected by the many strongly heterogeneous structures such as the subducting slab, mantle wedge, and the overlying crustal structure. We demonstrate that including 3D structure improves the estimation of key features of coseismic HR-GNSS time series, such as the peak ground displacement (PGD), the time to PGD (tPGD), static displacements (SD), and waveform cross-correlation values. We computed 1D and 3D synthetic, 0.25 Hz and 0.5 Hz waveforms at HR-GNSS stations for four M7.3+ earthquakes in Japan using MudPy and SW4, respectively. From these synthetics, we computed intensity-measure residuals between the synthetic and observed GNSS waveforms. Comparing 1D and 3D residuals, we observed that the 3D simulations show better fits to the PGD and SD in the observed waveforms than the 1D simulations for both 0.25 Hz and 0.5 Hz simulations. We find