A comparative study of physicochemical parameters and transport properties of the heteroaromatic polymer polybenzoxazinoneimide (PBOI) and its hydrolytically stable prepolymer, imide-containing polyamic acid (PI-PAA), has been performed. The process of thermal conversion of PI-PAA into PBOI has been studied using thermogravimetric analysis, differential scanning calorimetry, and mass spectrometry. The conversion of PI-PAA into PBOI increases the glass transition temperature and the density of the polymer, resulting in a reduction of fractional free volume. Both of the test polymers have been examined as membrane materials in pervaporation dehydration of aqueous isopropyl alcohol. It has been shown that PBOI is more effective in this process compared with the prepolymer. The transport properties of the PBOI membrane have been compared with published data on other polymers used in the pervaporative separation of the water–isopropanol azeotrope.