We present the characteristics of marine magnetic anomalies in the Nankai Trough and the northern Shikoku Basin. The marine magnetic anomalies are clearly visible over the Shikoku Basin but gradually disappear across the Nankai Trough. The expected reason for the decrease in the marine magnetic anomaly amplitudes across the trough is the increase in depth of the magnetic source: the subducting oceanic crust. Forward and inverse magnetic modeling results, which take into account the slab depth distribution, show variations in magnetization that cannot be explained solely by increasing depth of the slab. We identify five zones along the trough axis on the basis of the pattern of the magnetic amplitude profile: two ridges, a seamount chain, and two basement zones. The magnetic inversion analysis indicates cyclic intensity variations along the ridge zones. The largest contrast in magnetization along the N-S lineation before the deformation front occurs off Ashizuri (AS). Low-temperature chemical oxidation effects are most likely the main cause of the reduction in magnetization. There are considerable differences in the original carrier of magnetic intensity in the AS and Kii Peninsula (KP) zones, and the original carrier in AS is characterized by much higher original magnetic intensities. This indicates several possibilities: the oceanic crust originated from asymmetric spreading; there was magma injection during the late stage volcanism; or the AS zone was affected by an anomalous heat source. It would be concluded from the current data that the basement in AS originally had a much stronger magnetic carrier and suffered stronger low-temperature oxidation effects than the eastern part of the Shikoku Basin. The regional differences in intensity strongly suggest a variety of magnetic minerals and phase changes associated with temperature and mechanical dislocation.