Energy is often dissipated and released in the process of rock deformation and failure. To study the energy evolution of rock discontinuities under cyclic loading and unloading, cement mortar was used as rock material and a CSS-1950 rock biaxial rheological testing machine was used to conduct graded cyclic loading and unloading tests on Barton’s standard profile line discontinuities with different joint roughness coefficients (JRCs). According to the deformation characteristics of the rock discontinuity sample, the change of internal energy is calculated and analyzed. The experimental results show that under the same cyclic stress, the samples harden with the increase in the number of cycles. With the increase of cyclic stress, the dissipated energy density of each stage gradually exceeds the elastic energy density and occupies a dominant position and increases rapidly as failure becomes imminent. In the process of increasing the shear stress step-by-step, the elastic energy ratio shows a downward trend, but the dissipated energy is contrary to it. The energy dissipation ratio can be used to characterize the internal damage of the sample under load. In the initial stage of fractional loading, the sample is in the extrusion compaction stage, and the energy dissipation ratio remains quasi-constant; then the fracture develops steadily, the damage inside the sample intensifies, and the energy dissipation ratio increases linearly (albeit at a low rate). When the energy storage limit is reached, the growth rate of energy dissipation ratio increases and changes when the stress level reaches a certain threshold. The increase of the roughness of rock discontinuity samples will improve their energy storage capacity to a certain extent.