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, NaYF₄:50%Yb³⁺/2%Tm³⁺@NaYF₄@NaYF₄:20%Yb³⁺/2%Er³⁺@NaYF₄@NaYbF₄:2%Er³⁺ multilayered core-shell microcrystals are prepared by using multiple epitaxial growth through introducing surface modifiers and controlling their reaction conditions. The XRD and SEM results clearly show that the core-shell microcrystals possess a pure hexagonal crystal structure in the form of a disk. The microdesk has a thickness of about 2.32 μm and a diameter of about 28.31 μm. The upconversion luminescence characteristics of different single microcrystal structures are investigated by a confocal microspectroscopy system. In order to realize the selective excitation and emission of a single microcrystal, the spatial distribution of luminescent ions can be controlled through introducing 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 and 475 nm), red (648 nm) and green (524 and 540 nm) emissions are observed, which mainly originat from Tm³⁺ and Er³⁺ radiative transitions. Meanwhile, the red and blue upconversion emission intensities of the microcrystals are improved by using various shell layers. In addition, the luminescence and energy-transfer features of single microcrystals are explored by changing the excitation position. The experimental results demonstrate that the incorporation of NaYF₄ inert shells between luminescent layers can regulate luminescence and prevent ions from interacting. By utilizing the spectral fingerprint data of dopant ions in various shell layers, we create customizable micro-nano photonic barcodes and employ them for optical anti-counterfeiting detection. This study explores the use of constructed core-shell structures with luminescent tunable micron core-shell structures to acquire diverse spectral information and maintain stability through their structural properties. Thus, this core-shell structure provides a novel method for using upconversion luminescent microcrystals into micro- and nanophotonics to achieve anti-counterfeiting and display purposes.