Ionic liquids (ILs) are salts which persist in liquid state near room temperature. They are characterized by high thermal and chemical resistance, good solubility, and high ionic conductivity. ILs can be used as permeability enhancers for transdermal delivery of drugs. The study of the interaction of ILs with lipids is important for understanding their potential toxicity to cells and the environment. In this work, we discuss features of the molecular structure and mobility of the aqueous system consisting of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and ethylammonium nitrate ionic liquid (EAN) mixtures studied by NMR and computer simulation MD methods. The 31P NMR line shape analysis revealed two lipid states in the systems: in D2O it is a lamellar liquid crystalline state associated with the formed vesicle-like structures of DMPC, while in EAN it is isotopic. The ratio of these states correlates with the ratio of solvents in the system. Based on the self-diffusion coefficients obtained by NMR, sizes of the diffusing particles were estimated. The method of MD showed that DMPC molecules assemble into micelles in the presence of water. In the mixtures of EAN and water the configuration of DMPC molecules changed. When DMPC interacts only with EAN, the micelle disintegrates. It is thus inferred that the presence of IL in the environment significantly affects the structure of the lipid system. The comparative analysis of the SDCs revealed a correlation between values obtained by MD and NMR methods.