Poly(trimethylene terephthalate) (PTT)/poly(ethylene naphthalate) (PEN) blends of various compositions were prepared by the solution-blending and melt-blending methods. The changes in miscibility and crystallization behaviors of the blends upon thermal treatment above the melting temperature of the blends at $280^{circ}C$ were investigated by using DSC, DMA, $^1H$ NMR, and SAXS analyses. Without any thermal treatment, the blend systems were not miscible, and the thermal transitions, such as glass transition, cold crystallization, and crystal melting of the individual components were observed in the DSC and DMA analyses. With thermal treatment, though, they became miscible as the thermal transitions of each component disappeared and single glass transition peaks were observed in the thermal analysis. The chain randomness determined using $^1H$ NMR spectroscopy revealed that thermal treatment at $280^{circ}C$ for more than 30 min brought about transesterification reactions between the PTT and PEN segments resulting in an increase in their miscibility. These results were confirmed by the small angle X-ray analysis conducted to determine the long period (L), the thickness of the crystalline lamella stack ($l_c$), and the thickness of the amorphous region ($l_a$). After short thermal treatment, the melt-blended sample followed the values for the individual components. However, with extended thermal treatment, the blend became homogeneous, possessing different crystalline morphologies which resulted in different values of L, $l_c$, and $l_a$.