Physical unclonable functions (PUFs) enable different characteristics according to the purpose, such as easy to access identification, high security level, and high code capacity, against counterfeiting a product. However, most multiplex approaches have been implemented by embedding several security features rather than one feature. In this paper, we present a high security level anti-counterfeiting strategy using only labyrinth wrinkle patterns with different complexities, which can be used as unique and unclonable codes. To generate codes with different levels in a microtaggant, we fabricated wrinkle patterns with characteristic wavelength gradients using grayscale lithography. The elastic modulus of the polymer substrate and corresponding wavelength after the wrinkling process were controlled by designing the gray level of each subcode region in a gray-level mask image for photopolymerization of the microparticle substrate. We then verified the uniqueness of the extracted minutia codes through a cross-correlation analysis. Finally, we demonstrated the authentication strategies by decoding different minutia codes according to the scanning resolution during the decoding. Overall, the presented patterning method can be widely used in security code generation.