In this study, the real particle morphology of rockfill materials is obtained through three-dimensional scanning technology, and flexible boundary conditions are established by coupling the discrete element method and the finite element method. Then, a large-scale three-axis numerical simulation test is carried out on the rockfill materials to study the macroscopic mechanical properties and the change rule of the microscopic view of the rockfill materials in different characteristic states. The macroscopic results show that the stress–strain curves of the rockfill materials can be divided into softening and hardening curves. The phase transition, peak, and critical states of the softening-type curves show different mechanical properties, but no clear distinction between the characteristic state changes can be seen in the hardening-type curves. The microscopic results show that the displacement of the upper and lower parts of the flexible boundary of the softening curve increases with loading, and there is no obvious displacement in the middle part, but the middle particles undergo rotational deformation. An “X” shear band appears, and the strength of the force chain and the coordination number tend to increase first and then decrease. The flexible boundary displacements of the hardening-type curves are similar to those of the softening-type curves, but the central particles show a large number of cleavages instead of shear zones, and the force chain strength and coordination number levels show a continuous upward trend.