The construction of core-shell structure can effectively reduce the quenching effect on the surface of materials and realize the regulation of ion-ion interaction, which has become one of the effective ways to enhance and regulate the spectral characteristics of rare-earth upconversion luminescent materials. In this paper, a variety of NaYbF<sub>4</sub>: 2%Er<sup>3+</sup> micron core-shell structures were constructed with the help of epitaxial growth technology, which effectively enhanced the red upconversion emission of Er<sup>3+</sup>ions. The prepared microcrystals with core-shell structures are all hexagonal phase microdisks, and their sizes are relatively uniform. In order to better obtain the material spectral data, a confocal microscopic spectroscopy testing system was used to study spectral properties. Under 980 nm near-infrared laser excitation, the red emission intensity of single NaYbF<sub>4</sub>:2%Er<sup>3+</sup>@NaYbF<sub>4</sub>@NaYF<sub>4</sub>core-shell-shell microdisk is 4.6 times higher than that of NaYbF<sub>4</sub>:2%Er<sup>3+</sup> micron disk, and the red-to-green ratio is increased from 6.3 to 8.1. Meanwhile, Ho<sup>3+</sup> ions were introduced into the NaYbF<sub>4</sub>:2%Er<sup>3+</sup>@NaYbF<sub>4</sub>: 2%Ho<sup>3+</sup>@NaYF<sub>4</sub> core-shell-shell microdisk, and the red emission intensity was nearly 6.7 times higher than that of single NaYbF<sub>4</sub>: 2%Er<sup>3+</sup> microdisk, and the red-to-green ratio increased from 6.3 to 9.4 by means of ion-to-ion interaction. Through the study of microcrystal spectral characteristics and luminescence kinetics of different core-shell structures, showing that the red emission enhancement of Er<sup>3+</sup> ions is mainly derived from the construction of different core-shell structures, which can effectively enhance the cross-relaxation between Er<sup>3+</sup> ions, the energy back transfer between Yb<sup>3+</sup> and Er<sup>3+</sup> ions, and the energy transfer between Ho<sup>3+</sup> ions to Er<sup>3+</sup> ions. The micron core-shell structures with efficient red emission in this paper has great application prospects in the fields of luminescence, anti-counterfeiting and optoelectronic devices.