We developed a mechanical subducting plate model and re-examined the crustal deformation history in the Sagami Trough subduction zone, central Japan, the northernmost convergence boundary of the Philippine Sea Plate. The elevation distributions and formation ages of the Holocene marine terraces, representing past coseismic and long-term coastal uplifts, have been thoroughly investigated in this region. However, no physically consistent formation scenario to explain them has been demonstrated. Surface deformations within subduction zones are typically calculated using kinematic elastic dislocation models, such as the back-slip model. However, these models cannot explain permanent deformation after an earthquake sequence. This study develops a mechanical subducting plate model that balances the slips of interplate shear stress and can produce permanent deformations caused by a local bump geometry. We modeled earthquake recurrences by shear stress accumulation and coupling patches. As a result, we successfully reproduced the averaged uplift rate distribution estimated from the Holocene marine terraces. The findings suggest that the subducted seamount significantly affects long-term deformation patterns. In addition, the discrepancy between the elevation distributions and formation ages of Holocene marine terraces, which previous geological studies have indicated, can be interpreted by the rupture delay of coupling patches. This study also demonstrates that the traditional assumption of the back-slip model on the plate boundary for long-term subduction possibly results in an oversimplified model.