Current 3D micrometer-sized covert security labels are limited to simple designs involving graphics, texts, and numerical elements that constrain coding/decoding complexity and data density. Herein, we introduce photostable perylene dye-doped 3D security labels that feature intricate multimaterial and multilayered machine-readable quick-response (QR) codes fabricated using two-photon lithography (TPL). Leveraging precise label sizing and positioning, our innovative "QR codes-in-QR code" approach significantly enhances data storage capacity by over 250%. To bolster security, we employ a 2.0 μm thick 3D cover engraved with QR codes to conceal the 2D QR codes. We extend our advancements by introducing QR code-engraved 3D covers with stair-step patterns and 3D security labels featuring multimaterial, multilayered machine-decipherable QR codes. These 3D QR code-based security labels demonstrate minimal color and information interference and offer exceptional security levels. Even after 6 months of storage, they consistently provide repetitive readouts without degradation and photobleaching. These labels augment data concealment, decoding complexity, and photostability in enhancing their efficacy and longevity in data storage, communication, and anticounterfeiting applications.