We implemented molecular dynamics simulations to study the effect of single-walled carbon nanotube (SWCNT) and carboxylic (–COOH) functionalized SWCNT on the crosslinking and interfacial behavior of Epon 862 nanocomposite. Results showed that the introduction of control SWCNT in the Epon system reduced the crosslinking by 8–12% in comparison to control system (without CNT). The molecules of Epon 862 and Epikure-W changed their conformation and aligned themselves in the direction parallel to the surface wrapping the nanotubes. Also, no interfacial bonding was found between the polymer and SWCNT. However, the introduction of the –COOH functional groups on the surface of SWCNT lead to increase in crosslinking and resulted in a strong bond formation between the polymer and nanotube interphase. A significant increase in energy was found in Epon/COOH-SWCNT systems that lead to an increase of 33% in interfacial strength in comparison to Epon/SWCNT counterpart. The pullout simulations of Epon/SWCNT samples showed separation at the interphase with no polymer atoms attached to CNT. In contrast, bond stretching and breakage were observed in the polymer chain, whereas, a strong interphase was observed in Epon/COOH-SWCNT samples. This study reveals the nanolevel interactions between the nanotubes and polymers which otherwise not possible through experimental techniques, and lead to cognize that the functionalization of SWCNT with –COOH groups can establish a strong network with the epoxy chain and significantly enhance the interfacial properties particularly for applications where the interphase is critical.