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The multilevel encoding (MLE) scheme is an effective method for improving the anticounterfeiting encryption capabilities of physically unclonable functions (PUFs). However, owing to the correlation between encoding layers, the encoding capacity (EC) is difficult to improve by orders of magnitude. Herein, four noncorrelated structures in the diamond crystal structure (carbon–carbon single bond, defect luminescence structures, spin structures, and electron energy distribution structures) are considered for MLE. First, the microdiamonds containing nitrogen‐vacancy (NV) color centers are embedded into polydimethylsiloxane (PDMS) to fabricate PUFs. Using an optical imaging system, four codable images of four noncorrelated structures are read. The noncorrelation of the four‐level encoding structure is verified by calculating the Hamming distance (0.496 ± 0.02). The results show that EC exponentially improves to 24×10 000/(100 pixels)2. Furthermore, the encoding method based on the energy level does not depend on physical structure parameters, such as the size and position of the spin structure. Thus, it is protected from structural modeling attacks, resulting in high security. Moreover, PUF labels based on PDMS flexible substrates can be employed for various flexible applications. In the proposed scheme, the information is encrypted by a four‐level two‐dimensional (2D) barcode and decoded by self‐developed PUF authentication software. The proposed scheme presents a way for developing next‐generation PUFs with super‐high EC. [ABSTRACT FROM AUTHOR]