The present invention relates to a method of manufacturing a superparamagnetic nanocomposite and a superparamagnetic nanocomposite manufactured using the same, and more particularly to a method of manufacturing a superparamagnetic nanocomposite suitable for use in magnetic separation for the detection of a target biomaterial and a superparamagnetic nanocomposite manufactured using the same. The method of manufacturing the superparamagnetic nanocomposite according to the present invention has a higher yield and a high rate without complicated processing than a conventional method of manufacturing a magnetic nanoparticle for magnetic separation and is capable of mass production of the superparamagnetic nanocomposite having excellent properties with uniform size and particle size distribution, high aqueous solution dispersibility and high magnetization and being capable of maintaining superparamagnetism.