Detailed heat flow surveys were carried out in the central part of the Nankai Trough southeast of the Kii Peninsula (off Kumano) for investigation of the thermal structure of the subducting plate interface. At stations in the Kumano Trough (forearc basin) and its vicinity, long-term monitoring of temperature profiles in surface sediments was conducted because bottom water temperature variations (BTV) significantly disturb subbottom sediment temperatures. Heat flow values were successfully determined at seven stations by removing the influence of BTV from temperature records for 300 to 400 days. The surface heat flow data were combined with estimates from depths of methane hydrate bottom simulating reflectors to construct a heat flow profile across the subduction zone. Heat flow decreases from 90–110 mW/m2 on the floor of the Nankai Trough to 50–60 mW/m2 at around 30 km from the deformation front, while it is rather uniform, 40–60 mW/m2, in the Kumano Trough. The values measured on the Nankai Trough floor are concordant with the value estimated from the age of the subducting Philippine Sea plate, about 20 m.y., taking into account the effect of sedimentation. The obtained heat flow profile was used to constrain thermal models of the subduction zone. The subsurface thermal structure was calculated using a two-dimensional, steady state model, in which the frictional heating along the plate interface and the radioactive heat production are treated as unknown parameters. Comparison of the calculated surface heat flow in the Kumano Trough with the observed data indicates that the effective coefficient of friction is small, about 0.1 or less, and thus the shear stress on the plate interface is very low in this subduction zone.