Vitrinite reflectance study on the Cretaceous Shimanto accretionary prism of Southwest Japan shows that the vitrinite reflectance varies from 0.6% to 3.0%, corresponding to the estimated maximum paleotemperature variation of 90–210 °C. The thermal structure shows a sharp discontinuity across an out-of-sequence thrust separating it into two thermal blocks. In each block, vitrinite reflectance values increase systematically toward the prism younging direction, and the thermal structure is clearly overprinted on the tectonic imbrication of turbidite and melange units. This provided us with a set of data to calculate the geometry and displacement of the out-of-sequence thrust. The fission-track zircon partial-annealing ages indicate that this thrust was active about 43 Ma, probably in response to the accretion of Eocene rocks. This study shows that initial thickening of the accretionary prism, in an order of several kilometres, was mainly controlled by out-of-sequence thrust.