The effect of transreactions on the phase behavior in poly(ethylene 2,6-naphthalate) and poly(ethylene isophthalate) blends was investigated by using differential scanning calorimetry. The transreactions between two polymers were confirmed by H-1 nuclear magnetic resonance. At the beginning step of transreactions, the blend samples show two glass transitions. However, after transreactions occur to some extent (i.e., when the degree of randomness is >0.4), a single glass transition is observed. As the transreactions proceed, the composition difference between ethylene 2,6-naphthalate-rich and ethylene isophthalate-rich phases lessens. Additionally, the weight fraction of each phase decreases because of the increment of interfacial fraction with the lapse of reaction time.