As advanced physical cloning and cyber-extraction techniques proliferate, achieving absolute hardware-level information security has become a paramount global challenge. Conventional architectures systems are fundamentally vulnerable because deterministic memory and cryptographic hardware are physically decoupled, exposing sensitive data to interception. While physical unclonable functions (PUFs) offer robust authentication, integrating them with high-density data writing within a unified nanoscale medium remains elusive. Here, we present an intrinsically secure all-in-one architecture that inextricably fuses high-dimensional data encoding with multiscale physical encryption within single nanodiamonds (NDs). Through precise focused-electron-beam irradiation, we achieve single-nanoparticle defect engineering, enabling deterministic base-36 data writing within individual NDs. Crucially, this customized memory layer is permanently locked within the medium's inherent stochasticity, combining macroscopic spatial PUFs with strictly irreproducible atomic-scale quantum fingerprints extracted via optically detected magnetic resonance (ODMR). By seamlessly embedding deterministic memory into an unclonable physical environment, our approach intrinsically eliminates the vulnerabilities of separated hardware, providing an unconditionally secure solid-state foundation for tamper-proof memory chips, zero-trust networks and next-generation data vaults.