Rare earth upconversion nanoparticles have attracted considerable attention in the fields of display, detection, especially biomedicine because they can convert near infrared light into visible light. However, due to the limitation of upconversion luminescence mechanism and the electron transition characteristics of rare earth ions, the fluorescence quantum yield of rare earth upconversion nanoparticles is very low, which greatly limits theirs development. Therefore, it is very important to improve the luminescence efficiency of rare earth upconversion nanoparticles. Coating shell layer on rare earth upconversion nanoparticles by preparing core-shell structured materials can inhibit the surface quenching of rare earth materials, passivate lattice defects of the inner-core surface, isolate the interference of external adverse factors, which greatly improve the efficiency of transformation on the luminescence. Meanwhile, it can bring a series of excellent performance. For example, coating single-layer shell can change the material surface hydrophobicity; coating multilayer shells can prepare multifunctional nanocomposites with diagnostic and therapeutic function. Based onthe characteristics of rare earth ions and upconversion luminescence, the defects of rare earth upconversion nanoparticles were analyzed. This paper also focused on the advantages and disadvantages of several kinds of the preparation methods of core-shell structured nanomaterials which were widely studied in recent years, including inert core-shell structure, active core-shell structure and multilayer core-shell structure. The structural characteristics and application status of three types of core-shell structures were summarized. And their effects of core-shell structure on the luminescence of upconversion nanoparticles were discussed. We pointed out that the main effects of the inert shell on the fluorescence of the rare earth upconversion nanoparticles, including isolating the external environment interference and reducing the surface activity of the materials. Coating active shell on the surface can introduce new functions by doping different ions in the shell. Multi-layer shell can not only effectively prevent ion transition and reduce fluorescence quenching, but also provide new ideas for the preparation of integrated nanometer treatment platform for diagnosis and treatment by making full use of the advantages of rare earth materials and various treatment methods. Finally, we reviewed the applications of rare earth upconversion nanoparticles with core-shell-structure in deep tissue imaging, multi-mode imaging, drug delivery, photothermal therapy and photodynamic therapy. And we also pointed out the existing problems in development of core-shell-structured materials. For example, the bonding strength between shell and core was not easy to control; the optimum shell coating thickness was not uncertain; and the materials were not still industrialized. In the future, the emphasis should be put on exploring the mechanism of core-shell structure and seeking for more efficient methods of shell preparation based on the principles, in order to further expand the application of core-shell structured rare earth upconversion nanomaterials in biomedical fields. © 2019, Materials Review Magazine. All right reserved.