Poly(trimethylene terephthalate) (PTT)/poly(trimethylene naphthalate) (PTN) (50/50, weight ratio) blend films (T5N5) with amorphous state were prepared by melt-pressing of solution blended powders at $260^{circ}C$ for various times and quenching them in liquid nitrogen. Homo PTT and PTN films were also prepared by the same method. Small angle X-ray scattering (SAXS) measurements during the heating process were carried out using synchrotron X-ray source to investigate the changes in microcrystalline structure of the PTT, PTN and T5N5 films. From the electron density correlation functions obtained from SAXS patterns, long period (L), lamella thickness ($I_c$), and amorphous layer thickness ($I_a$) were calculated. Long periods of the amorphous films began to increase at around crystallization temperature of the samples. The increase in both $I_c;and;I_a$ attributed to the increase of L.L of PTN film is larger than that of PTT. L of T5N5 exhibited values between those of PTT and PTN film and it increased with heat treatment time at $260^{circ}C$.