Water-soluble silicon nanoparticles (SiNPs) have been synthesized with photoluminescence quantum yield more than 32% via a hydrothermal treatment of 3-aminopropyltriethoxysilane as silicon sources and maleic acid (MA) as surface-stabilizing ligands. Prepared SiNPs showed the presence of carboxylic acid groups through the incorporation of MA. The presence of 48.8 and 51.2% of Si-Si and Si-O binding was observed in the resulting carboxylic acid-functionalized SiNPs (COOH-SiNPs). As revealed by the fluorescence lifetime images, COOH-SiNPs possesses several fluorophores mainly composed of above Si-Si binding inside of single particle, which explains the excitation-dependent fluorescence emission behavior of COOH-SiNPs. Also, the presence of oxides mainly composed of Si-O binding and MA on the surface of COOH-SiNPs provides long-term stability for both fluorescence and dispersion. The potential use of COOH-SiNPs as fluorescence bioimaging agents for cellular media has been demonstrated. COOH-SiNPs showed excellent cell viability more than 91% for both MDAMB and MDCK cells even in 1,000 ppm concentration, and multicolor fluorescence imaging (blue, green, and red) of MDAMB cells was successfully accomplished with different excitation wavelengths.