The thermal behavior of the rigid amorphous phase (RAF) of poly (ethylene naphthalene-2, 6-dicarboxylate) (PEN) has been characterized well by differential scanning calorimetry (DSC). The RAF is supposed originating from an anisotropic interphase without lateral order between isotropic amorphous and crystalline phase. However, there were no direct proofs to confirm such suggestion. The kinetic mechanism of formation of the RAF has not been studied. In the present work, the identity of the RAF in molecular conformation was assured by Fourier transform infrared spectroscopy (FTIR). The kinetics of the formation of RAF was firstly traced by time resolved FTIR measurement, It was found that the RAF grew simultaneously with the growth of crystal, but had some delay in relatively low isothermal crystallization temperature. The study of Avrami's equation by FTIR spectroscopy was also carried out.