The extraction of natural gas hydrates is highly likely to cause the deterioration of the mechanical properties of energy soils. Fully understanding the mechanical properties of deep-sea energy soils is a prerequisite for the safe and efficient extraction of natural gas hydrates. In this study, the evolution of the stress-strain behavior of energy soils under different effective confining pressures and shear rates was analyzed through a combination of laboratory tests and discrete element numerical simulations. A triaxial shear discrete element model for energy soils was established using the PFC discrete element simulation software. The distribution patterns of contact force chains and particle displacement during the shear process of deep-sea energy soils were investigated, revealing the mesoscopic mechanism of the mechanical properties of energy soils. The results show that the shear strength of energy soils gradually increases with increasing effective confining pressure and shear rate. The higher the shear rate, the more pronounced the softening behavior of energy soils. During the shear process, the contact force chains between particles are gradually transferred from the ends of the specimen to the middle. As the effective confining pressure increases, the radial displacement of the particles decreases, leading to smaller macroscopic radial deformation of the specimen.