A multiscale modeling framework that integrates an atomistically informed damage model for carbon nanotube (CNT)-reinforced polymers is used to assess the mechanical property degradation, damage, and failure in adhesive bonded composite components with a CNT-enhanced adhesive layer. The atomistically informed damage model is developed using a continuum damage mechanics approach with varying CNT weight fractions. The developed damage model is implemented at the microscale using high-fidelity generalized method of cells (HFGMC) micromechanics accounting for the material constituents and imperfect interfaces. The micromechanical model is then coupled with a finite element simulation of a composite adhesively bonded T-Joint, achieving a nano-micro-macro multiscale analysis framework. This multiscale framework is validated using experimental observations at the macro and mesoscale whereby global load-displacement response and local strains are compared at critical structurally sensitive regions.