© 2017 Elsevier B.V. Methane hydrate is considered as a promising energy resource for the near future. To predict the gas productivity from the methane hydrate in the subsea sand-sediment, it is important to know effective permeability accurately of the sediment bearing methane hydrate. Hence, the hydrate morphological distribution: namely, what is the shape and morphology of hydrate, in the sediment should be elucidated, because the permeability is strongly affected by the hydrate distribution. In this study, to know where hydrate is formed in the pore of porous media, we proposed a numerical model for estimating the microscopic distribution of methane hydrate in sand sediment, using the classical nucleation theory and the phase-field model. The former theory gave the probabilities of hydrate nucleation positions in the gas-water-sand three-phases and the latter method provided the mobility of the front of the hydrate formation. A necessary hydrate formation rate constant was determined by history-matching with an experiment in the literature. Using the obtained rate constant, we numerically simulated hydrate formations within the microscopic computational domains.