This paper presents an atomistically informed approach to investigate the effects of temperature on material responses of carbon nanotube (CNT) reinforced nanocomposites. The molecular model of radially grown CNT reinforced polymer composites, also known as fuzzy fiber nanocomposites, has been developed by explicitly modeling the CNT, graphene-based carbon fiber and epoxy-based polymer matrix. A polymeric functional coating for the carbon fiber surface, which serves as a substrate for the CNT growth, is also explicitly modeled. Virtual deformation tests on the molecular model are performed to investigate the variation of mechanical properties at different temperature. The bond dissociation energy (BDE) obtained from the simulations can be directly interpreted as mechanical degradation due to covalent bond breakage. The results show accelerated bond breakage at high temperature. Mechanical instability is observed beyond a specific temperature, which can be correlated with the glass transition temperature of the system. This physics-based understanding of the effects of temperature on critical mechanical properties will be highly valuable for the design optimization of CNT reinforced nano-engineered composites.