The present invention relates to a method of preparing heavy metal nanoparticles using a heavy metal-binding protein. More specifically, relates to a method for preparing heavy metal structures, comprising the steps of: culturing a microorganism transformed with a gene encoding a heavy metal-binding protein, in a heavy metal ion-containing medium, to produce heavy metal structures in the microorganism; and collecting the produced heavy metal structures, as well as nanoparticles of heavy metal structures prepared according to said method. Unlike prior methods of preparing quantum dots by physically binding metal materials, the quantum dots disclosed herein can be efficiently produced by expressing the heavy metal-binding protein in cells. In addition, the quantum dots are useful because they can solve an optical stability problem that is the shortcoming of organic fluorophores.