The heat transport properties of aromatic polyimide thin films have become more important in the use for the electric insulation in the microelectronic devices with highly integrated circuits. The various kinds of measuring methods have been applied to obtain the anisotropic thermal conductivity and thermal diffusivity of thin films, however, if the specimens are soft and transparent, the conventional methodology requires highly advanced technology in preparing the specimens for the measurement and the results obtained vary widely. The purpose of this study is to apply the temperature wave analysis (TWA) method to measure the thermal diffusivity of thin films and spin-coated layers of aromatic polyimide in the thickness direction at various temperatures. The TWA is an absolute method to determine the thermal diffusivity by using the phase shift of temperature wave. We have performed measurements on the five different chemical structures of aromatic polyimide, including polyimide isoindoloquinazolinedione (PIQ), pyromellitic dianhydride and 4,4′-oxydianiline (PMDA/ODA), 3,3′,4,4′,-biphenyltetracarboxylic dianhydride and p-phenylenediamine (BPDA/PPDA), 3,3′,4,4′-biphenyltetracarboxylic dianhydride and 4,4′-oxydianiline (BPDA/ODA), and 3,3′,4,4′-benzophenonetetracarboxylic dianhydride and 3,3′-diaminobenzophenone (BTDA/DAB). As a result, thermal diffusivity of thin films in a thickness range from 0.1 to 300 μm at a temperature range from 10 to 570 K is obtained. The thickness dependence of thermal diffusivity of spin-coated layers of PIQ exhibits a good coincidence with the tendency of molecular anisotropy observed by attenuated total reflection Fourier transform infrared spectroscopy. In the low temperature below 20 K the amorphous PMDA/ODA film exhibits a substantial increase, which can be understood by considering the phonon mean free path of amorphous systems as first noted by Kittel for inorganic glasses. The glass transition of BTDA/DAB is observed as a rapid decrease of thermal diffusivity. The results indicate the availability of TWA for the present needs of accurate but simple measuring technique to determine the thermal diffusivity of thin polymer films, which is strongly dependent on the chemical and anisotropic structures.