Self-assembly offers a promising method to organize functional nanoscale objects into two-dimensional (2D) and 3D superstructures for exploiting their collective effects(1-3). On the other hand, many unique phenomena emerge after arranging a few nanoscale objects into clusters, the so-called artificial molecules(4-10). The strategy of using biomolecular linkers between nanoparticles has proven especially useful for construction of such nanoclusters(4-6,11-16). However, conventional solution-based reactions typically yield a broad population of multimers or isomers of clusters; furthermore, the efficiency of fabrication is often limited(4-6,11-16). Here, we describe a novel high-throughput method for designing and fabricating clusters using DNA-encoded nanoparticles assembled on a solid support in a stepwise manner. This method efficiently imparts particles with anisotropy during their assembly and disassembly at a surface, generating remarkably high yields of well-defined dimer clusters and Janus (two-faced) nanoparticles. The method is scalable and modular, assuring large quantities of clusters of designated sizes and compositions.