Carbon nanotube (CNT)-reinforced poly(ethylene 2,6-naphthalate) (PEN) nanocomposites were prepared by direct melt blending process in a twin-screw extruder. There is significant dependence of the crystallization and melting behavior of PEN/CNT nanocomposites on CNT content and crystallization temperature. The incorporation of CNT may favor the formation of the beta-form crystals in PEN/CNT nanocomposites, and more CNT content amplified this effect. In this PEN/CNT nanocomposite system, the CNT promoted the nucleation and the growth with higher crystallization rate of PEN/CNT nanocomposites, and simultaneously reduced the fold surface free energy and the work required in folding polymer chains in the polymer nanocomposites. In addition, the incorporation of a very small quantity of CNT significantly improved the mechanical properties of PEN/CNT nanocomposites.