In this paper, we study the crosslinking route and interfacial interactions for achieving superior properties in carbon nanotube (CNT)-reinforced epoxy-based nanocomposites by using multi-scale modelling. For that purpose, polymeric epoxy matrices consisting of EPON 862 epoxy and TETA hardener molecules were coarse-grained and simulated using the dissipative particle dynamics (DPD) method. Furthermore, CNTs were coarse-grained as rigid rods and embedded into the uncrosslinked mesoscopic polymer system. Reverse-mapping of the atomistic details onto the coarse-grained models was carried out to allow further simulations at the atomistic scale using molecular dynamics (MD) while keeping the periodicity of the CNTs’ structure. The mechanism of crosslinking was simulated, and both neat and CNT-reinforced thermoset nanocomposites with different degrees of crosslinking were reconstructed. Normal stresses in both tensile and compressive loading directions (up to 0.2% strain) were calculated, and the yield strength (at 0.2% offset) and compressive/elastic modulus in both normal directions are reported, which match well with experimental values. Overall, this paper explores a fast and straightforward procedure to bridge periodic mesoscopic structures, such as CNTs and their nanocomposites, to experimentally tested material properties.