In order to eliminate the undesirable characteristics of carbonaceous mudstone roadbed fillers, cement and fly ash are used to modify the pre-disintegrated carbonaceous mudstone, and the stress–strain relationship of pre-disintegrated carbonaceous mudstone before and after modification are analyzed by a series of conventional unconsolidated undrained triaxial compression tests at different confining pressures and different ages. Based on the microscopic modification mechanism of carbonaceous mudstone and the concept of binary medium model, the products from hydration reaction of pre-disintegrated carbonaceous mudstone, cement, and fly ash are regarded as bonded elements, and the pre-disintegrated carbonaceous mudstones without hydration reaction are regarded as frictional elements, and the binary medium model of modified pre-disintegrated carbonaceous mudstone is established. The results show that the stress–strain curve of pre-disintegrated carbonaceous mudstone is strain-hardening type, and the stress–strain of pre-disintegrated carbonaceous mudstone modified by fly ash and cement is strain-softening type, and the mechanical properties of modified pre-disintegrated carbonaceous mudstone are significantly improved. The deformation and damage mechanism of modified carbonaceous mudstone is investigated by applying the concept of binary medium model from a mesoscopic perspective, and the stress-bearing mechanism of bonded elements and frictional elements in external loading and stressing processes are analyzed. Finally, the measured data reveals that the binary medium model can simulate both the stress–strain softening characteristics of modified pre-disintegrated carbonaceous mudstone and the stress–strain hardening characteristics of organic material-modified expansive soils reasonably well.