A three-dimensional (3D) nanoplasmonic structure includes a substrate; a plurality of nanorods formed on the substrate; and a plurality of metal nanoparticles formed on surfaces of the substrate and the plurality of nanorods. A method of manufacturing a 3D nanoplasmonic structure includes preparing a substrate; growing a plurality of nanorods on the substrate; forming a metal layer on surfaces of the plurality of nanorods; and dewetting the metal layer into particles by heat-treating the metal layer