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We investigate crustal deformation in southwest Japan over a 3-year period revealed by a permanent dense Global Positioning System (GPS) array. Southwest Japan is a part of the Amurian Plate, a microplate moving about 10 mm/yr toward the east with respect to the Eurasian Plate. It overrides the Philippine Sea Plate at the Nankai Trough and collides with the northeast Japan arc in the central part of Japan. In this paper we first derive GPS site velocities relative to the stable part of the Amurian Plate in order to isolate signals of crustal deformation caused by the subduction and/or the collision. The velocity field has a conspicuous feature indicating the interseismic elastic loading by the Philippine Sea Plate slab at the Nankai Trough, characterized by the northwestward movements of points throughout the studied area. Their amplitudes are the largest at the Pacific coast and decay toward the Japan Sea coast with a subtle systematic shift of azimuths. A model assuming an elastic half-space, the convergence rate at the Nankai Trough based on a refined Euler vector, and the strength of the coupling inferred from a thermal model, could explain the velocity field in the western part of the studied area to a large extent. Those in the eastern part systematically deviate from them, and the residual components there show east-west shortening and north-south extension. This may represent crustal thickening and trenchward extrusion of crustal blocks caused by the collision between southwest and northeast Japan. This suggests that the collision between southwest and northeast Japan gives rise to not only crustal thickening but also trenchward extrusion of crustal block. A velocity contrast was found across the Median Tectonic Line, the largest inland active fault in Japan, but the current permanent GPS network is not dense enough for us to discuss its coupling depth.