A multi-level micromechanics-based homogenization is proposed here to investigate the damage behavior of composites with multiscale fibers such as carbon nanotube (CNT) and carbon fiber. First, a molecular unit cell is constructed considering the interfacial characteristics between the CNT and a polymer matrix, after which molecular dynamics simulation and micromechanics are utilized to obtain the elastic properties of CNT-reinforced composites. A micromechanics-based progressive damage model is then adopted to predict the damage behavior of the CNT and carbon fiber-reinforced composites. Tensile tests are also conducted to investigate the stress–strain behaviors of the composites. To verify the applicability of the proposed model, the present predictions are compared with those obtained from the tensile test results. The proposed multi-level homogenization has shown to provide a close match to the experimental results. The proposed modeling scheme may facilitate a thorough investigation of the damage behavior of multiscale fiber-reinforced composites, proving the importance of each constituent at a different level.