The rare-earth doped micro/nano core-shell structure not only is beneficial to enhancing the upconversion emission intensity, but also can realize the fine control of luminescence color through the spatial separation of ions. In this work, a series of NaYF ₄@NaYF ₄core-shell (CS) microcrystals doped with different ion concentrations is constructed by using the epitaxial growth technology. The structure and morphology for each of the prepared microcrystals are characterized by X-ray diffractometer (XRD) and scanning electron microscope (SEM). The experimental results show that the prepared CS structures each have a pure hexagonal-phase crystal structure, and exhibit a disk-like shape. Under the excitation of 980 nm laser, the energy transfer characteristics of doped ions in single CS microcrystal are carefully studied by using a confocal microscope spectroscopy test system and changing the excitation position. The study shows that the ions doped in different regions of the CS microdisks exhibit different spectral characteristics when the excitation position is changed, which is mainly due to the different directions of excitation energy transfer in the CS structure. Based on the emission spectra of different positions and power variation spectra, it is proved that the excitation energy of the micron CS is mainly transmitted from outside to inside. Meanwhile, the colorful emission pattern of the CS microdisk is revealed by the corresponding optical waveguide model, which is mainly due to the optical waveguide effect. Therefore, by constructing different micron core-shell structures, the luminescence characteristics of microcrystals can be controlled and adjusted, which can provide important experimental reference for the applications of microcrystals in optoelectronic devices, optical coding and multicolor display.