Liquid crystal emulsion is a new type of emulsion, in which the emulsifier molecules are located at the oil/water (O/W) interface and form a long-range ordered and short-range disordered lamellar liquid crystal. The lamellar liquid crystal formed by the emulsifier is similar to the skin stratum corneum lipid structure, which enables it to have a broad application prospect in the fields of cosmetics, pharmaceuticals, etc. In this work, a liquid crystal nanoemulsion was obtained by passing a liquid crystal emulsion stabilized by hydrogenated lecithin and phytosterol combination through a microfluidizer. The microstructure of the prepared liquid crystal nanoemulsion was investigated experimentally by dynamic light scattering, transmission electron microscopy, and small-angle X-ray scattering. The results have shown that the nanoemulsion inherited the liquid crystal emulsion property, namely, the long-range ordered and short-range disordered lamellar structure still existed at the oil/water interface even though they underwent extrusion, friction, and acceleration. At the same time, the underlying mechanisms of the existence of lamellar liquid crystal between the oil phase and the water phase for the nanoemulsion were explored theoretically by molecular dynamics simulations. The simulation results elucidated that the hydrogenated lecithin and phytosterol combination improved the flexibility of the bilayer structure composed of emulsifiers. The bilayers were the basic structure units of lamellar liquid crystals, and thus, the improved flexibility of bilayers provided insurance for the existence of lamellar liquid crystals with larger curvature around the oil droplets. In addition, the applicable properties of liquid crystal nanoemulsion were studied, and the results have shown that the liquid crystal nanoemulsion presented better slow-release and moisturizing properties than traditional nanoemulsions due to the existence of multilayers between oil and water phases. This work not only provides necessary information for the development and effective application of liquid crystal emulsions but also is helpful for in-depth understanding the inner properties of lamellar liquid crystal at molecular level.