Interpenetrating polymer networks based on biocompatible components—polyurethane and copolymer of 2-hydroxyethyl methacrylate with methacryloyloxyethylyphosphorylcholine (HEMA-MPC) were synthesized and thermodynamic parameters of interactions in the system, dynamic mechanical properties, porosity of the samples, morphology and physico-mechanical properties were investigated. The thermodynamic parameters of interactions between polymer components of the IPNs were calculated based on isotherms of methylene chloride vapors sorption by samples and it is shown that MPC plays the role of a compatibilizer in the system, increasing the thermodynamic compatibility between polyurethane and the HEMA-MPC copolymer at small amounts of the copolymer in the IPNs. As the amount of copolymer HEMA-MPC in the IPNs increases, the value of the free energy of the polyurethane and copolymer mixing moves to the positive value, which is associated with the formation of ionic clusters of MPC. By dynamic mechanical properties investigations have shown that created IPNs are two-phase systems with incomplete phase separation. The results of the morphology investigations of the IPNs samples are consistent with the data of the thermodynamic compatibility study of polymers during the formation of the IPNs. With a significant increase in the positive values of the free energy of the polyurethane and copolymer mixing in the IPNs with 41% and 51% of the copolymer content, a significant phase separation was observed in the IPNs, with phase inclusions ranging from 1 to 5 μm. Good physico-mechanical properties of the IPNs based on biocompatible components—polyurethane and copolymer of 2-hydroxyethyl methacrylate with methacryloyloxyethylyphosphorylcholine and existence of transition pores of size from 26 to 35 Å allow to assume that created materials can be used as biomedical coatings.