The recent availability of Global Positioning System‐Acoustic seafloor geodetic observations enables us to resolve the spatial distribution of the slip deficit rate near the Nankai trough, southwestern Japan. Considering a tectonic block model and the transient deformation due to the major earthquakes in this area, the slip deficit rate between the two relevant blocks can be estimated. In this study, we remove the time‐dependent postseismic deformation of the 2004 southeastern off the Kii Peninsula earthquakes (MJMA 7.1, 7.4), which had led to the underestimation of the slip deficit rate in earlier studies. We model the postearthquake viscoelastic relaxation using the 3D finite element model with bi‐viscous Burgers rheology, as well as the afterslip on the finite faults. The corrected Global Positioning System‐Acoustic and land‐based Global Navigation Satellite Systems data are aligned to the existing tectonic model and used to estimate the slip deficit rate on the plate boundary. We then calculate the coseismic displacements and tsunami wave propagation with the simple assumption that a hundred years of constant slip deficit accumulation was released instantaneously. To evaluate the influence of uncertainties in the plate interface geometry on a tsunami model for the Nankai trough, we investigated two different geometries and performed checkerboard inversion simulations. Although the two models indicate roughly similar results, the peak height of the tsunami wave and its arrival time at several points are significantly different in terms of the expected hazard.