Origin of a conspicuous microscopic fabric of a granitic pluton in the eastern part of southwest Japan, which has been an autochthonous component of the East Asian margin since the late Mesozoic, was elucidated through well-organized rock magnetic and geochronological investigations. The voluminous Late Cretaceous Toki Granite suffered a thermochemical event succeeding to its emplacement, which resulted in tightly grouped principal axes of the anisotropy of magnetic susceptibility (AMS). The magnetic fabrics originate from ferromagnetic and paramagnetic minerals precipitated upon the surface of fractures developed under regional tectonic stress. Together with previous studies of three-dimensional microcrack generation and intrusion sequence of dike swarms in the Toki Granite, temporal changes in the azimuths of AMS principal axes delineate a drastic shift in tectonic stress regime along the Asian continental margin from the Late Cretaceous to the Paleocene. This remarkable event is probably linked to a regional unconformity contemporaneously formed on the convergent margin.