GPS velocities in the vicinity of the Nankai Trough, southwest Japan, were inverted into three components: interplate loading due to Nankai Trough subduction, deformation associated with deep slip on the Median Tectonic Line (MTL), and the residual rigid plate motion. The results show a gradual decrease of interplate seismic coupling between 25 and 40 km depth on the Nankai Trough interface. This is consistent with the deep slip model, in which the fault extends as a ductile shear zone, with a depth‐variable interplate strain accumulation rate. The top 20 km of the interface may not be fully coupled, although the resolution is poor there. The low coupling at shallow depths is consistent with the accretionary prism detected by seismic surveys. The MTL slip rate is estimated to be between 0.00 and 5.50 mm/yr if we assume a vertical fault and between 0.00 and 3.88 mm/yr if we assume a north dipping fault. Combining our results with a geological estimate (4–9 mm/yr) and a geodetic estimate with a denser network (∼5 mm/yr) suggests that the MTL slip rate may be near the upper bound of our geodetic estimate, that is, ∼4–5 mm/yr. The rigid plate motion with respect to the stable Eurasian craton was estimated to be very small, indicating that southwestern Japan is on the Eurasian plate rather than a separate plate.