Recently, DNA has been used to guide the self-assembly of functional materials. Based on programmability of DNA, branched DNA nanostructures were created and precisely labeled with quantum dots and gold nanoparticles. The precise molecular recognition of DNA allows the precise design and synthesis of multifunctional hybrid materials by building DNA nanostructures. The first step of obtaining multi-functionality is to precisely label function materials on DNA building block or branched DNA before construction of complicated nanostructures. In this paper, we introduce the two routes to label functional nanoparticle on DNA structure. Quantum dots were successfully conjugated on branched DNA by streptavidin-biotin interaction and gold nanoparticles were attached on the DNA nanostructure by hybridization.