A method of synthesizing biogenic elemental selenium nanostructure using Enterobacter cloacae and its application. The method uses E. cloacae Z0206 to reduce selenite to zero valence selenium and forms nano-sized elemental selenium particles, including steps of inoculating activated E. cloacae Z0206 to fermentation broth, adding sodium selenite solution, shaking and incubating, collecting the fermentation broth and separating the elemental selenium nanoparticles.