Liquid-liquid phase separation and subsequent homogenization during annealing in an extruded poly(ethylene terephthalate) (PET)/poly(ethylene-2,6-naphthalate) (PEN) blend were investigated with time-resolved light scattering and optical microscopy. In the initial stage, the domain structure was developed by demixing via spinodal decomposition. In the later stage, the blend was homogenized by transesterification between the two polyesters. The crystallization rate depended on the sequence distribution of polymer chains, which was determined by the level of transesterification rather than the composition change of separated phases. When the crystallization of PEN preceded that of PET, PEN showed a higher melting point. However, when the crystallization rate of PEN was slower than that of PET, the previously formed PET crystals suppressed the crystallization of PEN, causing the coarse crystalline structure of PEN to have a lower melting point.