For a tsunami inversion analysis, we incorporated a new technique that uses many Green’s functions to improve model spatial resolution. Since this method precisely reproduces observed tsunami waveforms, we can obtain a better model of the tsunami source process. We applied the proposed method to the 2004 off the Kii Peninsula earthquake to determine what fault or faults ruptured to cause the earthquake. The estimated coseismic sea-surface deformation extended to two directions, and it was consistent with the distributions of the two aftershock swarms. Hence, we concluded that the earthquake resulted from the rupture of two faults.