Clusters have an atomically precise structure and possess functions significantly different from those of atoms, nanocrystals, and bulk solids. Here, we report a strategy of fabricating cluster nanodots and nanodot supracrystals based on the self-assembly principle of lipids. Firstly, we synthesized a pyramid Janus heterocluster consisting of two types of clusters [polyoxometalate (POM) and polyhedral oligomeric silsesquioxane (POSS)] covalently linked by a dendritic linker. Subsequently, the heterocluster self-assembled into core-corona nanodots in which individual POSS clusters distribute on the surface of a POM core in the POSS-preferred solvent. The nanodots further self-assembled into nanodot supracrystals as the solvent gradually evaporated. Reconstruction of the structural characteristics of the supracrystals by coarse-grained molecular simulations confirmed this two-step self-assembly process. Mathematical analysis indicated that solvation promotes the discontinuous distribution of individual POSS clusters on the surface of the POM cores. The results of this work will open up prospects for the preparation of artificial virus-like nanodots and highly ordered cluster-assembled nanomaterials for advanced applications.