Development of advanced fluorescent materials for constructing a secure and unclonable encryption is urgently required; however, their application in anti-counterfeiting applications is a great challenge. In this work, we proposed and synthesized a new type of upconversion nanoparticles@carbon dots@meso-SiO2 nanohybrids by integrating two fluorescent materials of lanthanide-doped NaYF4 upconversion nanoparticles (UCNPs) and carbon dots (CDs) into mesoporous silica (mSiO2) to produce a novel sandwichlike core-shell structure and a dual-mode fluorescence from UCNPs and CDs. By tailoring the UCNP core of different upconversion luminescence, all three kinds of dual-mode luminescent UCNPs@CDs@mSiO2 nanohybrids exhibited typical RGB upconversion luminescence under a 980 nm laser and blue downconversion luminescence under a 365 nm UV light. Due to strong the hydrophilic nature of the nanohybrids, they can be further fabricated into environmentally benign luminescent inks for creating highly secured, fluorescent-based, three-dimensional anti-counterfeiting barcodes via inkjet printing. The resultant UCNPs@CDs@mSiO2 inks with a dual-mode and tunable luminescence nature endow the inkjet-printing barcodes with an extremely high encoding capacity and high security. Such dual-mode fluorescent inks and barcodes are simple to fabricate, easy to view, efficient for coding, and difficult to clone, thus making them promising nanomaterials for anti-counterfeiting applications.