There is provided an organic-inorganic composite material containing a single nanoparticle therein, which is prepared by individually dispersing hydrophilic inorganic nanoparticles having a uniform particle size and conjugating biodegradable polymers to the surface of the nanoparticle, and a method of preparing the same. More particularly, the preparation method of the present invention comprises the following steps: 1) preparing hydrophilic nanoparticles by conjugating organic substances having a thiol group and a hydrophilic amine group to the surface of a core or a core/shell inorganic nanoparticle protected with a surfactant through a metal-thiolate (M-S) bond between them; 2) adjusting the concentration of the hydrophilic nanoparticles prepared in step 1) to 2.times.10.sup.-6 M or less and treating them in a sonication bath to prepare individually dispersed nanoparticles in the form of a single particle; and 3) conjugating biopolymers to the nanoparticle individually dispersed in step 2) through the formation of an amide bond between them under treatment in a sonication bath. The organic-inorganic composite material of the present invention exhibits high efficient photoluminescence and photostability as well as excellent chemical stability, dispersibility in water, biocompatibility and targetibility. Thus, it can be effectively used as a raw material for bioimaging or film coating.