Influence of methane hydrate on permeability of hosting sediments is critical to understand natural hydrate formation and gas production. A few conceptual models proposed to explain the influence of hydrate could not recapitulate the actual hydrate pore habits and distribution with the overly-simplified geometric assumptions used in those models. This study simulates single phase flow through hydrate-bearing sediments with a numerical approach to explore influences of hydrate on fluid flow, based on real 3D pore structures of methane hydrate-bearing sediments obtained via micro-CT scans. Pore-scale analysis and observations show (1) hydrate particles, at low hydrate saturation, protrude into the flow channels and efficiently inhibit the flow; (2) at high saturation or in small pores, hydrate particles block some pores and pores without hydrate determine permeability. Influence of intra-pore habit on permeability is not obvious; by contrast, inter-pore distribution of hydrate has a higher impact and can cause drastic permeability anisotropy.