First, the micro-bond contact model considering hydrate cementation thickness of the deep-sea methane hydrate soil proposed by Jiang et al. was applied to describe micro-bond contact mechanical properties of hydrate between methane hydrate soil particles. Second, the model is introduced into the discrete element method (DEM) by using C++ language to program it. Third, based on the selected hydrate saturation, the corresponding hydrate cementation size is obtained through actual adjustable calculation of two dimensional DEM simulation to revise the values of hydrate critical bond thickness, minimum bond thickness and bond width, then micro-bond parameters are determined. Finally, based on the parameters of methane hydrate, many biaxial tests with different hydrate saturations are carried out to simulate the mechanical properties of deep-sea methane hydrate soils. In addition, comparisons are made between triaxial experimental observations done by Masui et al. and numerical simulation from aspects of stress-strain, volumetric, dilatancy angle of methane hydrate soils. The results show that the macromechanical properties of deep-sea methane hydrate soils are reflected qualitatively by using hydrate micro bond model considering bond thickness; peak shear strength, cohesive force and dilatancy angle of deep-sea energy soil increase with increasing content of hydrate; but the influence of hydrate saturation on internal friction angle is uncertain; peak shear strength, residual shear strength and volume shrinkage increase with increasing effective confining pressure while dilatancy angle decreases.