The incorporation of functionalized nano‐fillers into epoxy‐based composites shows a potential to improve material performances, which based on the modification mechanism is well understood. In this study, amine functionalized multiwall carbon nanotube (MWCNT‐NH2) as an example was prepared and selected as a type of functionalized nano‐fillers to modify two kinds of tri‐functionality epoxy resins, i.e. diglycidyl‐4, 5‐epoxycyclohexane‐1, 2‐dicarboxylate (DGEAC) and n, n‐diglycidyl‐4‐glycidy‐loxyaniline (TGPAP). The interfacial interaction of MWCNT‐NH2 with DGEAC or TGPAP was investigated by using molecular dynamics (MDs) simulations. Further investigation on how the interfacial interactions affected the dispersion of MWCNT‐NH2 in each epoxy resin was conducted and their effects on the mechanical properties of the resulting nanocomposites were characterized. The MD simulation results indicated that a higher interfacial strength between MWCNT‐NH2 and TGPAP molecule was formed, no matter with non‐covalent or covalent interaction, due to the presence of benzene ring and nitrogen atom in the backbone of TGPAP molecule. Moreover, the experimental results showed that the stronger binding strength of MWCNT‐NH2 with TGPAP can bring more positive effect on the dispersion of MWCNT‐NH2 in the TGPAP‐based resin matrix, and then resulting in the considerable improved tensile toughness compared with the neat sample and MWCNT‐NH2 reinforced DGEAC‐based ones. POLYM. COMPOS., 39:E2552–E2561, 2018. © 2018 Society of Plastics Engineers