The phase transition behavior isothermal micro-phase separation kinetics of polyester-based thermoplastic elastomer were studied using the synchrotron X-ray scattering(SAXS) method. The structural changes occurring during heating period were investigated by determining the changes of the one-dimensional correlation function, interfacial thickness and Porod constant. Based on the abrupt increases of the domain spacing and interfacial thickness, a major structural change occurring well below the melting transition temperature is suggested. Those changes are explained in terms of melting of the thermodynamically unstable hard domains or/and the interdiffusion of the hard and soft segments in the interfacial regions. SAXS profile changes during the micro-phase separation process were also clearly observed at various temperatures and the separation rate was found to be sensitively affected by the temperature. The peak position of maximum scattering intensity stayed constant during the entire course of the phase separation process. The scattering data during the isothermal phase separation process was interpreted with the Cahn-Hilliard diffusion equation. The experimental data obtained during the early stage of the phase separation seems to satisfy the Cahn-Hilliard spinodal mechanism. The transition temperature obtained from the extrapolation of the diffusion coefficient to zero value turned out to be about 147$pm$$2^{circ}$, which is close to the order-disorder transition temperature obtained from the Porod analysis. The transition temperature was also estimated from the inveriant growth rate. By extrapolating the inveriant growth rate to zero, a transition temperature of about 145$pm$$pm$$2^{circ}$ was obtained.