The carbon fiber/polymer matrix interphase region plays an important role in the behavior and failure initiation of polymer matrix composites and accurate modeling techniques are needed to study the effects of this complex region on the composite response. This paper presents a high fidelity multiscale modeling framework integrating a novel molecular interphase model for the analysis of polymer matrix composites. The interphase model, consisting of voids in multiple graphene layers, enables the physical entanglement between the polymer matrix and the carbon fiber surface. The voids in the graphene layers are generated by intentionally removing carbon atoms, which better represents the irregularity of the carbon fiber surface. The molecular dynamics method calculates the interphase mechanical properties at the nanoscale, which are integrated within a high fidelity micromechanics theory. Additionally, progressive damage and failure theories are used at different scales in the modeling framework to capture scale-dependent failure of the composite. Comparisons between the current molecular interphase model and existing interphase models and experiments demonstrate that the current model captures larger stress gradients across the material interphase. These large stress gradients increase the viscoplasticity and damage effects at the interphase which are necessary for improved prediction of the nonlinear response and multiscale damage in composite materials.