The influence of methane hydrate on the permeability of hosting sediments is critical to understand natural hydrate formation and gas production. Reported experimental data from tests on laboratory synthesized hydrate-bearing specimens and hydrate-bearing cores retrieved from natural reservoirs spread in a large range, and often deviates from predictions of a few conceptual models. This is very likely due to the mismatch between the actual hydrate pore habits and distribution and 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 pore habit in single pores on permeability is not obvious; by contrast, distribution of hydrate in the overall pore network has a higher impact and can cause drastic permeability anisotropy. Heterogeneity in both hydrate distribution and the sediments can explain the widespread range of relative permeability as a function of hydrate saturation.