Poly(trimethylene terephthalate-co-trimethylene 2,6-naphthalate)s (P(TT-co-TN)s) with various copolymer composition were synthesized, and their chain structure, thermal property and crystalline structure were investigated by using $^1$H-NMR spectroscopy, differential scanning calorimetry (DSC) and wide-angle X-ray diffraction (WAXD), respectively. It was found from sequence analysis that all the P(TT-co-TN) copolymers synthesized have a statistical random distribution of TT and TN units. It was also observed from DSC thermograms that the glass transition temperature increases linearly with increasing the TN comonomer content, whereas the melting temperature of copolymer decreases with increasing the corresponding comonomer content in respective PTT- and PTN-based copolymer, showing pseudo-eutectic melting behavior. All the samples melt-crystallized isothermally except for P(TT-co-66 mol % TN) exhibit multiple melting endotherms and clear X-ray diffraction patterns. The multiple melting behavior originates from the dual lamellar population and/or the melting-recrystallization-remelting. The X-ray diffraction patterns are largely divided into two classes depending on the copolymer composition, i.e., PTT and PTN $eta$-form diffraction patterns, without exhibiting cocrystallization.