Poly(ethylene 2,6-naphthalate)/multi-walled carbon nanotube (PEN/MWNT) nanocomposites are prepared by in situ condensation polymerization in the presence of various acid-treated MWNT (a-MWNT) contents and their morphology, rheological and mechanical properties are investigated as a function of the a-MWNT content. SEM image of a plasma-etched nanocomposite exhibits that a-MWNTs are dispersed well in the PEN matrix by forming an interconnected network structure. Accordingly, rheological properties such as complex viscosities and shear moduli of PEN/a-MWNT nanocomposites at the terminal region of low frequency are much higher than those of pure PEN. Glass transition temperatures of nanocomposites also increase with the increment of the a-MWNT content, which stems from the reduced chain mobility due to the specific interaction between a-MWNTs and PEN matrix. Dynamic and tensile mechanical properties of nanocomposites are also higher than those of pure PEN and they increase with the increment of the a-MWNT content. The highly improved mechanical properties of PEN/a-MWNT nanocomposites are explained to originate from the interconnected network structure of a-MWNTs in PEN matrix as well as the strong interfacial adhesion between a-MWNTs and PEN matrix.