The critical challenge for preparing carbon nanotube (CNT)/polymer nanocomposites is how to create a strong interfacial binding energy (IBE) between the polymer matrix and the CNT. Molecular dynamics simulations of nylon 6 melts and its composite with pristine CNT or functionalized CNT embedded have been performed. The properties of the nanocomposites are investigated with the IBE between CNT and nylon 6. The non-bond energies from both vdW and electrostatic interactions, are calculated for nylon 6 and CNT functionalized by different groups. Our calculational results show that the vdW interaction energies of all the functionalized CNT/nylon 6 composites are close to that of the pristine CNT/nylon 6 composite, implicating the electrostatic interactions are responsible for the strong IBE of the functionalized CNT/nylon 6 composites. Therefore, the functionalized CNT can expand the application of polymer in actual production.