A numerical model of mesoscopic nonhomogeneous random aggregate with multiple contact models is constructed based on discrete element theory to study the fine-view damage mechanism of the road subgrade under fatigue loading. The damage accumulation-energy dissipation method is proposed for the first time to analyze structural damage behavior from the perspective of energy change and mesoscopic damage accumulation. The feasibility of the numerical analysis model was validated by using a three-dimensional discrete element model to simulate the uniaxial compression test of cement-stabilized macadam and compare it with the test results for verification. Subsequently, a fatigue damage test model is established to test the macroscopic mechanical properties and observe the mesoscopic damage in the concrete model structure. This was combined with a comparative analysis of each energy dissipation law. The peak stress, peak strain, and peak elastic modulus errors in uniaxial compression simulations are 0.67%, 5.06%, and 6.96%, respectively. The friction energy is much larger than the impact and damping energy, and the growth trend of all three is the same in the medium term. Moreover, a linear increase phase is observed with an increasing number of cycles. In the cyclic loading simulation, only 0.47% irrecoverable strain is generated during the 20th-122nd cycles. The linear bonded contact damage is more severe in the first period, and the largest damage factor difference is 21.85%. The kinetic energy reached a maximum value of 0.46 J in the first cycle, and then fluctuated regularly with cyclic loading and maintains a decreasing trend until the specimen is finally crushed, and kinetic energy increases again. This study provides a new approach for the fatigue damage analysis of CSM.