Information security serves as the cornerstone for ensuring the stable development of today’s highly digitized era. As cryptographic primitives with high security and robust encryption capabilities, physical unclonable functions (PUFs) are recognized as one of the critical solutions to address information leakage issues. However, the encoding of PUFs often relies on the inherent properties of materials, which limits the potential for further enhancement of their encoding capacity (EC). In this study, we introduce a four-level encoding scheme by leveraging the stochastic characteristics of free radical chemical reactions and energy deposition in the fabrication process of silicon carbide (SiC) color centers. A multilevel multimodal PUF (MMPUF) encoding strategy (ES) for flexible substrates with high EC, low cost, and simple and fast readout was constructed. The spatially random distribution of SiC and silicon vacancy (V_si) color-center concentrations as well as the offsets of the laser pyrolysis position along the X- and Y-axes are four independent physical properties that ensure the encoding performance of the PUF, achieving a high encoding capacity of 2^4×10×10 and secure, stable, and unclonable encoding. Furthermore, the integration of the PUF tags with the products through a doping manufacturing process, rather than simple attachment, enhances the security and practicality of the anti-counterfeiting system. The proposed encoding hierarchy based on the offsets provides a novel encoding solution for improving PUF EC.