Colloidal crystallization using DNA provides a robust method for fabricating highly programmable nanoparticle superstructures with collective plasmonic properties. Here, we report on the DNA-guided fabrication of 3D plasmonic aggregates from polydisperse gold nanoprisms. We first construct 1D crystals via DNA-induced and shape-directed face-to-face assembly of anisotropic gold nanoprisms. Using the near-Tm thermal annealing approach that promotes long-range DNA-induced interaction and ordering, we then assemble 1D nanoprism crystals into a 3D nanoprism aggregate that exhibits a polycrystalline morphology with nanoscale ordering and microscale dimensions. The presence of closely packed nanoprism arrays over a large area gives rise to strong near-field plasmonic coupling and generates a high density of plasmonic hot spots within the 3D nanoprism aggregates that exhibit excellent surface-enhanced Raman scattering performance. The plasmonic 3D nanoprism aggregates demonstrate significant SERS enhancement (<106), and low detection limits (10-9M) with good sample-to-sample reproducibility (CV ∼ only 5.6%) for SERS analysis of the probe molecule, methylene blue. These findings highlight the potential of 3D anisotropic nanoparticle aggregates as functional plasmonic nanoarchitectures that could find applications in sensing, photonics, optoelectronics and lasing.