Morphology in an extruded poly(ethylene terephthalate)/poly(ethylene-2,6-naphthatate) was investigated using time-resolved light scattering, optical microscope and small-angle X-ray scattering. During annealing at 280 degreesC, the domain structure via spinodal decomposition preceded, the transesterification followed, and then the transesterification between the two polyesters induced the dissolution of the liquid-liquid (L-L) phase separation, i.e. the homogenization. The annealed specimen for various time periods (t(s)) at 280 degreesC was subjected to a temperature-drop to 120 degreesC for the isothermal crystallization and then the effects of liquid phase morphology on crystallization was investigated. With t(s) the H-nu (cross-polarization) light scattering patterns exhibited the dramatic change from a four-leaf clover pattern with maximum intensity at azimuthal angle 45degrees (X-type scattering pattern) to a diffuse pattern of circular symmetry and then a four-leaf clover pattern with maximum intensity at azimuthal angles 0 and 90degrees (+-type scattering pattern). This suggests that the crystalline structure depends on the level of the block and/or random copolymer produced by the transesterification during annealing. The H, scattering patterns reflected differences in the principle polarizability of the crystalline lamellae with respect to the spherulitic radius. On the other hand, the long period L-B, an average distance between two adjacent crystalline lamellae, increased with t(s) at 280 degreesC The dependence of L-B on t(s) was explained by the change in the crystallization rate G.