We investigated the effects of various viscoelastic structures on postseismic surface displacement and principal strain fields associated with the great 1946 Nankaido earthquake, which occurred on the plate boundary between the subducting Philippine Sea plate and the continental Eurasian plate. For this purpose, we constructed two kinds of three-dimensional structural models using the finite element method: one is the Layered Model, in which a semi-infinite Maxwell viscoelastic material is underlying an elastic layer, and the other is the more realistic Plate Model, in which the three-dimensional configuration of the subducted Philippine Sea plate is taken into account. We also considered two cases with different thicknesses of the elastic layer (50 and 33 km) for the respective models. The difference between the two models in postseismic surface deformations is significant for the case with the thinner elastic layer. In this case the horizontal surface displacement and principal strain for the Layered Model is two to three times larger than those for the Plate Model. Downward surface deformation tends to be dominant for the Layered Model, while the change in the pattern for the Plate Model is less marked. The spatial extent of uplift and subsidence for the Plate Model is broader than that for the Layered Model. Postseismic vertical displacements in Shikoku were found to be strongly dependent on the viscoelastic structures. From these results, we suggest that the estimates of the viscosity of the uppermost mantle, interplate coupling, and the area and the amount of after-slip following the 1946 Nankaido earthquake, which have been estimated based on simple layered viscoelastic models, should be re-evaluated using realistic three-dimensionally heterogeneous viscoelastic structures.