A series of poly(butylene terephthalate-co-butylene 2,6-naphthalate) (P(BT-co-BN)) random copolymers were synthesized, and their cocrystallization behavior was investigated by differential scanning calorimetry (DSC) and wide-angle X-ray diffraction (WAXD). The P(BT-co-BN) copolymers, which are found to be statistical random copolymers, show a single melting and a single crystallization peak over the entire range of copolymer composition and have a eutectic melting point in the plot of melting point versus composition. WAXD patterns of copolymers are divided into two groups, i.e., the PET type crystal and the PEN type crystal. These facts indicate that the P(BT-co-BN) copolymers show isodimorphic cocrystallization. The eutectic composition at which the crystal transition between PET and PEN type crystal occurs was estimated ca. 35 mol % BN content. When the defect free energy was calculated by using the equilibrium inclusion model, the defect free energy (6.10 kJ/mol) in the case of incorporation of BN units in the PET type crystal was higher than the opposite case (3.63 kJ/mol). It means that the incorporation of bulkier BN units in the PET type crystal is more sterically hindered than the opposite case. The changes of heat of fusion and d spacings with composition also support isodimorphic crystallization.