Highly flexible, transparent, and luminescent nanofibrillated cellulose (NFC) nanopaper with heterogeneous network, functionalized by rare-earth up-converting luminescent nanoparticles (UCNPs), was rapidly synthesized by using a moderate pressure extrusion paper-making process. NFC was successfully prepared from garlic skin using an efficient extraction approach combined with high frequency ultrasonication and high pressure homogenization after removing the noncellulosic components. An efficient epoxidation treatment was carried out to enhance the activity of the UCNPs (NaYF4:Yb,Er) with oleic acid ligand capped on the surface. The UCNPs after epoxidation then reacted with NFC in aqueous medium to form UCNP-grafted NFC nanocomposite (NFC-UCNP) suspensions at ambient temperature. Through the paper-making process, the assembled fluorescent NFC-UCNP hybrid nanopaper exhibits excellent properties, including high transparency, strong up-conversion luminescence, and good flexibility. The obtained hybrid nanopaper was characterized by transmission electron microscopy (TEM), atomic force microscope (AFM), Fourier transform infrared spectroscopy (FTIR), field emission-scanning electron microscope (FE-SEM), up-conversion luminescence (UCL) spectrum, and ultraviolet and visible (UV-vis) spectrophotometer. The experimental results demonstrate that the UCNPs have been successfully grafted to the NFC matrix with heterogeneous network. And the superiorly optical transparent and luminescent properties of the nanopaper mainly depend on the ratio of UCNPs to NFC. Of importance here is that, NFC and UCNPs afford the nanopaper a prospective candidate for multimodal anti-counterfeiting, sensors, and ion probes applications.