Organic and inorganic hybrid nanocomposites based on poly(ethylene 2,6-naphthalate) (PEN) and silica nanoparticles were prepared by a melt blending process. In particular, polymer nanocomposites consisting mostly of cheap conventional polyesters with very small quantities of inorganic nanoparticles are of great interest from an industrial perspective. The crystallization behavior of PEN/silica hybrid nanocomposites depended significantly on silica content and crystallization temperature. The activation energy of crystallization for PEN/silica hybrid nanocomposites was decreased by incorporating a small quantity of silica nanoparticles. Double melting behavior was observed in PEN/silica hybrid nanocomposites, and the equilibrium melting temperature decreased with increasing silica content. The fold surface free energy of PEN/silica hybrid nanocomposites decreased with increasing silica content. The work of chain folding (q) for PEN was estimated as $7.28{ imes}10^{-20}J$ per molecular chain fold, while the q values for the PEN/silica 0.9 hybrid nanocomposite was $3.71{ imes}10^{-20}J$, implying that the incorporation of silica nanoparticles lowers the work required to fold the polymer chains.