Methane gas hydrate (MGH) is an important clean energy source. In submarine continental margins, the main hydrate occurrence in the sediment is the pore-filling type, and there is a huge difference in the sediment particle shape. Thus, in this study, with a new algorithm based on X-ray computed tomography (CT), 16 three-dimensional models were reconstructed with different hydrate saturations and particle shapes. Pore network modeling (PNM) was used to characterize the pore space evolution, and the impacts of various hydrate saturations and particle shapes on the other physical properties were studied using PNM and the finite volume method (FVM). It is found that (1) when both the sediment particle size and the hydrate saturation are certain, the hydrate-bearing sediment (HBS) with rounder particles presents a smaller average radius of the pore and throat, (2) when hydrate saturation increases, the tortuosity appears as an upward trend and the HBS with irregular particles presents a faster increased rate, (3) when hydrate saturation becomes higher and higher, the permeability of HBS emerges as a downward trend and the HBS with rounder particles presents a lower permeability, (4) under the same hydrate saturation, the HBS with rounder particles presents a higher apparent thermal conductivity, and (5) the electrical conductivity of HBS will gradually decrease as hydrate saturation increases, and the HBS with rounder particles presents a lower electrical conductivity and a higher resistivity.