Active and passive seismic experiments in the Kii Peninsula, southwest Japan, revealed prominent structural features around the segment boundary of a megathrust earthquake associated with the subduction of the Philippine Sea Plate (PHS). A distinct reflection band in the uppermost part of the PHS shows significant lateral variation along its strike. The thicker reflection band, which corresponds to the deeper extension of the fault area of the 1944 Tonankai Earthquake, is interpreted to be a zone of high pore fluid pressure, causing a state of conditionally stable slip on the plate boundary by the reduction in effective normal stress. A thinner reflective band corresponds to the deepest part of the rupture area of the 1946 Nankai earthquake, where plate coupling is stronger due to less effect of fluids. This along-strike structural variation controls the differences in frictional properties and the lateral limit of rupturing along the plate boundary.