A methodology that accurately simulates the brittle behavior of epoxy polymers initiating at the molecular level due to bond elongation and subsequent bond dissociation is presented in this paper. The system investigated in this study comprises a combination of crystalline carbon nanotubes (CNTs) dispersed in epoxy polymer molecules. Molecular dynamics (MD) simulations are performed with an appropriate bond order-based force field to capture deformation-induced bond dissociation between atoms within the simulation volume. During deformation, the thermal vibration of molecules causes the elongated bonds to re-equilibrate; thus, the effect of mechanical deformation on bond elongation and scission cannot be captured effectively. This issue is overcome by deforming the simulation volume at zero temperature—a technique adopted from the concept of quasi-continuum and demonstrated successfully in the authors’ previous work. Results showed that a combination of MD deformation tests with ultra-high strain rates at near-zero temperatures provides a computationally efficient alternative for the study of bond dissociation phenomenon in amorphous epoxy polymer. In this paper, the ultra-high strain rate deformation approach is extended to the CNT-epoxy system at various CNT weight fractions and the corresponding bond disassociation energy extracted from the simulation volume is used as input to a low-fidelity continuum damage mechanics (CDM) model to demonstrate the bridging of length scales and to study matrix failure at the microscale. The material parameters for the classical CDM model are directly obtained from physics-based atomistic simulations, thus improving the accuracy of the multiscale approach.