The base of the methane hydrate stability zone (MHSZ) in the Kumano Basin, offshore Japan, is marked by a bottom-simulating reflection (BSR) on seismic data. At Integrated Ocean Drilling Program Site C0002, which penetrates this BSR, the in situ temperature profile combined with bulk seawater methane equilibrium conditions suggest that the base of the MHSZ is 428 m below seafloor (bsf), which is 28 m deeper than the observed BSR (400 m bsf). We found that submicron pore sizes determined by mercury injection capillary pressure are sufficiently small to cause 64% of the observed uplift of the base of the MHSZ by the Gibbs-Thomson effect. This is the most thorough characterization of pore sizes within the MHSZ performed to date and illustrates the extent to which pore size can influence MHSZ thickness. Our results demonstrate the importance of considering lithology and pore structure when assessing methane hydrate stability conditions in marine sediments.