<p>The reduction in permeability of sediments due to blockages caused by suspended fine particles is a common concern for the extraction processes of oil, natural gas, or methane gas from methane hydrate. In this study, the permeability reduction caused by suspended fine particles was newly modelled. Solid–water two-phase flow in frame sand sediment was numerically simulated by a three-dimensional Lattice Boltzmann method. For frame sand, shapes of real sand grains were extracted by series expansion of spherical harmonics from CT-scan images and packed in a microscopic computational domain. For each fine particle, a motion equation is solved using the pressure integrated on its surface with considering its collision to the frame sand surfaces. The calculated relative permeability could not be modelled solely by the volume saturation of the fine particles, but also their specific surface area was required.</p>