Competitive domain-structure development and homogenization under annealing were investigated via time-resolved light scattering and H-1 n.m.r. in melt-quenched blends of partially miscible poly(ethylene naphthalene-2,6-dicarboxylate) (PEN) and poly(ethylene terephthalate) (PET) loaded with/without PEN-PET random copolymer as a compatibilizer. In the early stage the domain structure formation took place presumably by demixing via spinodal decomposition (SD). In the intermediate stage, the domain growth was retarded by transesterification between the two polyesters through the domain interphase, and the whole system was gradually homogenized due to the miscibility enhancement by the produced PEN-PET multiblock copolymer species, as revealed by H-1 n.m.r. analysis. Incorporation of the random copolymer also suppressed the domain growth and resulted in acceleration of the homogenization.