Relationship between structure and transport properties of two polyheteroarylenes is studied on the example of polybenzoxazinoneimide (PBOI) and its prepolymer–polyamic acid imide-containing (PAAI). Formation of dense membranes, determination of their physical parameters, and control of membrane morphology by SEM were carried out. Transport properties of the membranes in the separation of the water–ethanol mixture were determined by sorption and pervaporation experiments. The equilibrium sorption degree, diffusivity, as well as sorption selectivity and diffusion selectivity of the PAAI and PBOI membranes were considered. The pervaporation experimental data on the total flux and the separation factor of the membranes were converted into permeability and selectivity to estimate the performance of the membranes. Due to the–COOH groups in the structure, PAAI membrane exhibits significantly higher sorption degree of water (4 times more) and ethanol (10 times more) as compared with those of PBOI. However, the PAAI membrane has water/ethanol sorption selectivity lower than 1, which indicates the absence of separation efficiency in the ethanol dehydration. In contrast, the PBOI membrane is very effective in the ethanol dehydration as the separation factor reaches 9000 in pervaporation of the mixture containing 10 wt% water.