The construction of core-shell structures with different structural properties based on the epitaxial growth technique has become an effective technique for regulating the luminescence properties of micro/nanocrystals. In order to obtain richer spectral information, this work attempts to prepare NaYF ₄:50%Yb ³⁺/2%Tm ³⁺@NaYF ₄@ NaYF ₄:20%Yb ³⁺/2%Er ³⁺@NaYF ₄@NaYbF ₄:2%Er ³⁺multilayered core-shell microcry- stals by using multiple epitaxial growth with the introduction of surface modifiers and controlling their reaction conditions. From the XRD and SEM results, it is evident that the core-shell microcrystals possess a pure hexagonal crystal structure in the form of a disk.The microdisk has a thickness of about 2.32 μm with a diameter of about 28.31μm. The upconversion luminescence characteristics of different single microcrystal structures were investigated by a confocal microspectroscopy system. In order to achieve the selective excitation and emission of a single microcrystal, the spatial distribution of luminescent ions can be controlled through the introduction of an intermediate isolation layer. Under 980 nm laser excitation, different excitation sites of the single microdisk exhibit different upconversion emission characteristics. The significant blue (450 nm and 475 nm), red (648 nm) and green (524 nm and 540 nm) emissions are observed, mainly originating from Tm ³⁺ions and Er ³⁺radiative transitions. Meanwhile, the red and blue upconversion emission intensities of the microcrystals were improved by using various shell layers. In addition, the luminescence and energy-transfer features of single microcrystals were explored by varying the excitation position. The experimental results demonstrate that the incorporation of NaYF ₄inert shells between luminescent layers can regulate luminescence and prevent ion interactions. By utilizing the spectral fingerprint data of dopant ions in various shell layers, we created customizable micro-nano photonic barcodes and employed them for optical anti-counterfeiting detection. This study explores the use of constructed core-shell structures with luminescent tunable micron core-shell structures to achieve diverse spectral information and maintain stability through their structural properties. Thus, this core-shell structure offers a novel approach for utilizing upconversion luminescent microcrystals in micro- and nanophotonics for anti-counterfeiting and display purposes.