Carbon dioxide capture and storage is an efficient technology to reduce CO2. Among CO2 storage methods, storage in the form of gas hydrate is thought to be promising for increasing the volume capacity of storable CO2. Microscopic hydrate distribution within the pore space of sand sediment essentially controls its effective permeability coefficient. This study aimed to make a mathematical model of the effective permeability coefficient, using microscopic numerical method series that consists of packing sand grains within microscopic computational domains, arranging water and CO2 phases in the pore space of the packed sand grains, placing multiple hydrate nuclei, growing hydrate in the pores of the sand grains, and simulating single phase flow through the pore space of the packed sand grain and the formed hydrate, regarding the hydrate as a solid. The effect of heat diffusion on the reservoir scale is newly incorporated into the simulation method to continue the hydrate growth to high hydrate saturation. The computational results indicated the effects of hydrate distribution in the pore space on hydrate saturations, initial water saturations, and contact angles of water on the sand surface. Then, based on the results of the simulations, the effective permeability coefficient was modelled based on the Kozeny-Carman model, using simple polynomial equations.