This article discusses a molecular simulation of membrane processes for the separation of liquid mixtures during pervaporation. A method for simulating the structure of polyurethane membranes was developed. The method was based on the known mechanisms of the formation of macromolecules from constituent monomers. For the formation of a chemical bond between the monomers, values of the parameters of the potentials of intermolecular interactions were set so that bonds were formed only between the corresponding atoms. The algorithm was validated to produce polymer films from diphenylmethane diisocyanate (MDI) and amino ethers of boric acid (AEBA). The polymer film obtained according to the developed algorithm was used to study the adsorption of ethanol and water. The concentration distributions of the components inside the polymer film were obtained for films of various thicknesses. Modifications of the DCV-GCMD method were proposed for the molecular simulation of pervaporation. The algorithm was based on maintaining a constant density of the mixture in the control volume. After the molecules were added to the control volume, thermodynamic equilibrium was established. During this process, molecules moved only in the control volume, while the rest of the molecules were fixed. The proposed algorithm was used to calculate the flows of water and ethanol through the polymer film.