An atomistic methodology to simulate the constituent interphases in carbon fiber reinforced CNT/epoxy nanocomposites is presented in this paper. Two critical interphase regions are considered in the study: CNT/polymer interphase and the fiber/matrix interphase. The elastic and inelastic responses of the interphases are investigated through molecular dynamic (MD) simulations with appropriate force fields, and integrated with an atomistically informed multiscale modeling framework. The elastic behavior is studied at the molecular level using harmonic force fields whereas bond elongation and subsequent bond dissociation in epoxy polymer chains, and the fiber/matrix interphase are investigated using a bond order based force field. An MD simulation approach adopted from the concept of quasi-continuum (QC) is employed to calculate the bond dissociation energy during virtual deformation tests. The variation of bond dissociation energy density during the deformation tests is integrated into a continuum damage mechanics model to characterize microscale damage in the epoxy matrix. Furthermore, the atomistic forcedisplacement behavior is also extracted to formulate a tractionseparation law for the microscale cohesive zone models for the fiber/matrix interface.