A substrate for sensing, a method of manufacturing the substrate, and an analyzing apparatus including the substrate are provided. The substrate for sensing includes: a support layer; a plurality of metal nanoparticle clusters arranged on the support layer; and a plurality of perforations arranged among the plurality of metal nanoparticle clusters. The plurality of metal nanoparticle clusters each comprise a plurality of metal nanoparticles stacked in a three-dimensional structure. Each of the plurality of perforations transmits incident light therethrough.