A translucent wooden substrate with long-lasting phosphorescence, high photostability and durability, tough surface, ultraviolet protection, high optical transmittance, and superhydrophobicity was developed. This long-lasting phosphorescent wooden substrate is able to continue emitting light for extended time periods. Lignin-modified wood (LMW) was immobilized with a solution of epoxy resin (ER) and rare-earth doped aluminate (REDA) phosphor nanoparticles (NPs). For an improved dispersion of pigment, REDA was synthesized in a nanoscale particle size, and characterized by transmission electron microscopy (TEM) to indicate a particle size of 8–14 nm. The crystal structure of REDA nanoparticles was also proved by X-ray diffraction (XRD). For an improved production of long-persistent phosphorescent colorless woods, REDA must be well-dispersed in MAA without aggregation. Absorption and emission, as well as decay and lifetime spectra were explored. The morphologies of the wooden substrates with different ratios of REDA were investigated by scanning electron microscopy (SEM), X-ray fluorescence (XRF) analysis, Fourier transform infrared spectra (FT-IR), elemental mapping, and energy-dispersion X-ray (EDXA). The phosphorescent woods show changes in color from colorless to green under ultraviolet (UV) irradiation, and to yellowish-green in the dark, as proved by the colorimetric parameters of the CIE Lab system. The afterglow wood samples display an absorbance band at 365 nm and two phosphorescent bands at 431 and 520 nm. Improved UV shielding, photostability, and hydrophobicity were explored. With increasing REDA ratio, both static contact and slide angles are found to improve in the ranges of 147.6°–163.6° and 9°–14°, respectively. The long-lasting photoluminescence is optimized at a REDA ratio of 8%. The present strategy shows a large-scale production approach of multiple functional woods for many potential applications, such as smart glow in the dark windows and safety signs.