This technology features compositions of biocompatible silicon nanoparticles and methods of manufacturing such nanoparticles, which comprises the steps of forming a silicon nanoparticle colloid by ultrasonic treatment of Si-containing Zintl salt in diethylene glycol diethyl ether (DGDE), and introducing hydroxyl groups into the surface of the silicon nanoparticle by treating the silicon nanoparticle colloid with a halogenated hydrogen solution. The method of the present invention can easily mass-produce silicon nanoparticles having high dispersion stability in an aqueous solution and biocompatibility in a high yield.The objects of developing this technology are to provide such particles for use in researches for manufacturing nano-sized biostructures and biomedical applications.