We used three-component surface velocities in southwest Japan to estimate plate coupling on the subducting plate interface at the Nankai trough. We analyzed continuous GPS data from the Japanese GEONET network from 1996 to 2006 using a consistent analysis strategy that generates bias-fixed solutions for the entire network. We applied systematic time-series analysis methods to estimate common mode error, which improved position solutions for the entire network. To allow for differences in regional deformation sources, we modelled the plate coupling on the plate interface beneath Shikoku island to Kii Peninsula and the Tokai-Suruga trough separately. The results show strong coupling at a depth of ∼10–30 km off Shikoku and Kii Peninsula. The spatial variation in plate coupling coincides well with the coseismic rupture zones of the past large earthquakes. Maximum slip deficit rates of ∼2–3 cm yr −1 at the depth of ∼5–25 km are found beneath the Tokai area, consistent with results from other studies. The downdip limits of the highly coupled areas and transition zones beneath Shikoku and the Kii Peninsula correspond approximately to estimates of the 450 °C isotherms. Good correlation is observed between the lateral variations of the slip deficit distribution, low frequency earthquakes, and coseismic slip. This correlation suggests that temperature, and possibly fluid variations, contribute to such correlation in space. The interplate slip deficit derived from the GPS velocities over the 10 yr of observations is generally compatible with the results over shorter time spans, suggesting that plate coupling in SW Japan does not change significantly over the period of these GPS measurements.