Due to increasing global energy demands, research is being conducted on the mechanical properties of methane hydrate-bearing soils (MHBSs), from which methane hydrate (MH) will be explored. This paper presents a numerical approach to study the mechanical properties of MHBSs. The relationship between the level of MH saturation and the interparticle bond thickness is first obtained by analyzing the scanning electron microscope images of MHBS samples, in which is the bridge connecting the micromechanical behavior captured by the DEM with the macroscopic properties of MHBSs. A simplified thermal-hydromechanical (THM) bond model that considers the different bond thicknesses is then proposed to describe the contact behavior between the soil particles and those incorporated into the discrete element method (DEM). Finally, a series of biaxial compression tests are carried out with different MH saturations under different effective confining pressures to analyze the mechanical properties of deep-sea MHBSs. The results of the DEM numerical simulation are also compared with the findings from triaxial compression tests. The results show that the macromechanical properties of deep-sea MHBSs can be qualitatively captured by the proposed DEM. The shear strength, cohesion, and volumetric contraction of deep-sea MHBSs increase with increasing MH saturation, although its influence on the internal friction angle is obscure. The shear strength and volumetric contraction increase with increasing effective confining pressure. The peak shear strength and the dilation of MHBSs increase as the critical bond thickness increases, while the residual deviator stress largely remains the same at a larger axial strain. With increasing the axial strain, the percentage of broken bonds increases, along with the expansion of the shear band.