Marine hydrate reservoirs are an important form of natural gas, and investigating the permeability of hydrate reservoirs is of great significance for their development. During hydrate exploitation, both water saturation and hydrate saturation dynamically change, inducing a complicated variation in the permeability of hydrate reservoirs. Previous studies lacked specific conclusions on the effects of multiphase saturations on permeability in muddy hydrate-bearing reservoirs. This study remolded 9 cores with different water moisture values (0−14.5%) within a core holder using South Sea Clay and controlled water conversion (0− 61.1%) and hydrate saturations (8.63−42.16%) by the temperature agitation method. Based on Darcy's law, the permeabilities of water/hydrate-containing muddy reservoirs under different saturations were measured. It is found that the permeability decreases with the increase in both hydrate and water saturations, and the dynamic permeability of muddy cores with water conversion to hydrate is K = 40.71•e −41.26•w − (1.65−12.12•w)•χ. By inferring the increase in hydrate saturation at the same decrease in permeability, the ratio of hydrate and water saturations inducing an equivalent change in permeability is found as 1.18. The relationship between the permeability of muddy cores and contained hydrate and water saturations is established as K = 18.1•((1− 1.18•S h − S w )/(1 + 2•(1.18•S h + S w ))) 2.5 . This study is important for the dynamic prediction of the hydrate exploitation process.