Poly(ethylene terephthalate-co-ethylene naphthalate) (PETN)/organoclay was synthesized with the solution intercalation method. Hexadecylamine was used as an organophilic alkylamine in organoclay. Our aim was to clarify the intercalation of PETN chains to hexadecylamine-montmorillonite (C-16-MMT) and to improve both the thermal stability and tensile property. We found that the addition of only a small amount of organoclay was enough to improve the thermal stabilities and mechanical properties of PETN/C-16-MMT hybrid films. Maximum enhancement in both the ultimate tensile strength and initial modulus for the hybrids was observed in blends containing 4 wt % C-16-MMT. Below a 4 wt % clay loading, the clay particles could be highly dispersed in the polymer matrix without a large agglomeration of particles. However, an agglomerated structure did form in the polymer matrix at a 6 wt % clay content.