A novel route to the preparation of luminescent silica nanoparticles and coloration for living cells was demonstrated in this article. A europium-substituted polyoxometalate was encapsulated by a hydroxyl-group-terminated double-chain quaternary ammonium cation through an ion replacement process, yielding an organic-inorganic complex with core-shell structure bearing hydroxyl groups located at the periphery. The introduction of -OH groups not only increased the solubility of the complex in polar solvents but also caused it to embed into the inner matrix of silica nanoparticles covalently and be well-dispersed through an in situ sol-gel reaction with tetraethyl orthosilicate. Elemental analysis and spectral characterization confirmed the formation of prepared complexes with the anticipated chemical composition. Scanning and transmission electron microscopy images illustrated the size change of luminescent nanoparticles with smooth surfaces and well-dispersed polyoxometalate complexes inside of the silica matrix. X-ray photonic spectra and zeta-potential measurements revealed the chemical association between the silica matrix and the complex. Luminescent spectral characterization indicated the well-retained photophysical property of Eu-substituted polyoxometalate in silica nanoparticles. The surface amino-modified silica nanoparticles were applied to cell coloration, and the dyed Hella cells were observed through laser confocal fluorescence microscopy.