Heat flow values were estimated in the Nankai Trough fore-arc slope region off Kii Peninsula from the Bottom-Simulating Reflector (BSR) and other data obtained during IODP Expeditions 315 and 316. The heat flow has an uncertainty of approximately 20% mainly due to ambiguities in the temperature estimate at the BSR and uncertainties on the thermal conductivity. BSRs occur intermittently in the Imbricate Thrust Zone (ITZ). They are significantly shallower below anticlines, designated "Anticlinal High Zone" (AHZ), than in the adjacent synclines ("Basal Low Zone" (BLZ)). The heat flow in the BLZ (55-65 mW/m (super 2) ) is consistent with the regional heat flow trend. The shallow BSR in the AHZ produces an apparent high heat flow anomaly of 70-90 mW/m (super 2) , and discontinuities are observed across thrust faults. The most likely cause is the transient effect of thrust faulting followed by erosion on the hanging wall side. A one-dimensional time-dependent numerical model, with latent heat for hydrate and gas transition considered, indicates that the relaxation time for the BSR to reequilibrate after such a disturbance is approximately 10 kyr. Although the possibility that the shallow BSR is a remnant base of hydrate stability zone cannot be ruled out, if the shortening has occurred in the recent 10 kyr the convergent rate at the ITZ would be approximately 30 m/kyr, which is much larger than the recent horizontal shortening across the megasplay fault, and could even exceed the portion of the plate convergence than that accommodated at the frontal thrust.