The northeastern Japan arc is located in a typical subduction zone and is a seismically active region where large interplate earthquakes have occurred repeatedly. The nationwide GPS network has made it possible to investigate the crustal deformation in unprecedented detail; however, vertical displacements are less accurate than the horizontal ones and have not been used to constrain interplate coupling models. In this study, GPS carrier phase data are analyzed in order to estimate three components of site displacements. The result indicates uplift along the Japan Sea coast and subsidence along the Pacific Ocean coast. Using the vertical site velocities together with the horizontal ones as the data for a geodetic inversion method, a new model of interplate coupling is constructed to explain both the horizontal and vertical velocities for the interseismic period from 1997 to 2001. The model demonstrates strong coupling in the area off Miyagi and in the area off Aomori through the area off Tokachi, including the areas of asperities. The downdip limit of the locked fault zone on the plate boundary has been estimated seismologically to be at a depth of 50–60 km in northeastern Japan, and the distribution of slip deficits derived in this study indicates that the transition zone extends down to a depth of about 100 km.