This paper presents the measurement of the thermal constants of natural methane hydrate-bearing sediments and mud layer samples recovered from wells. Core samples were recovered from the Tokai-oki test wells (Nankai Trough, Japan) in 2004. The thermal conductivity, thermal diffusivity, and specific heat of the samples were simultaneously determined using the hot-disk transient method. The thermal conductivity of natural hydrate-bearing sediments decreased slightly with increasing porosity. In addition, the thermal diffusivity of hydrate-bearing sediments decreased as the porosity increased. Moreover, we also used simple models to calculate the thermal conductivity and diffusivity. Estimations of the distribution model (geometric mean model) were relatively consistent with the measured results, suggesting that sand grains and hydrates should be independently distributed for hydrate-bearing sediments, which exhibit a pore-filling pattern. The measurement results were also consistent with the thermal diffusivity, which was estimated by dividing the thermal conductivity obtained from the distribution model by the specific heat taken from the arithmetic mean. Finally, our estimate of the thermal conductivity of silt soil was much lower than that for sand soil in hydrate-bearing sediment, which suggests that the small grains influence thermal conductivity.