Morphology in an extruded poly(ethylene terephthalate)/poly(ethylene-2,6-naphthalate) was investigated using time-resolved light scattering, optical microscope and small-angle X-ray scattering. During annealing at 280 o C, 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 o C was subjected to a temperature-drop to 120 o C for the isothermal crystallization and then the effects of liquid phase morphology on crystallization was investigated. With t s , the H ν (cross-polarization) light scattering patterns exhibited the dramatic change from a four-leaf clover pattern with maximum intensity at azimuthal angle 45 o (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 90 o (+-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 ν 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 o C. The dependence of L B on t s was explained by the change in the crystallization rate G.