Size-dependent properties define a hallmark characteristic of nanomaterials, enabling scientists and engineers to create materials with tunable properties. Nanocrystal systems have been extensively studied and modeled to understand the synthesis and structure-property relations. Despite efforts to forge understandings, nanocrystals still possess a disparity in size/shape (although small) that in essence is a distribution of products, thereby convoluting their reaction pathway and understanding. At the limit of a truly monodisperse product, magic-size clusters (MSCs) are renowned for their identical size and precise composition, existing at an intermediate length scale between small molecule and conventional nanocrystal (i.e., nuclei). MSCs provide a quintessential framework to understand colloidal synthesis and to bridge structural transformations across all length scales. The origin of the MSC stability was thought to derive from the “closed-shell” arrangement of atoms; this inhibits the continuous growth that is typically seen with nanocrystals. We find that the MSC stability is strongly coupled to an organic-inorganic mesophase: a fibrous self-assembly of inorganic clusters passivated with organic ligands that form during high concentration (1000 mM) synthesis. This mesophase behaves as a large suspended network (>100 nm grains) that stabilizes and promotes a well-defined reaction pathway for the formation of high-purity MSCs. Although resistant to typical growth and dissolution processes, we demonstrate that perturbing (e.g., ligand exchange, solvent exposure, and shearing) the organic surface of CdS MSC induces a structural transformation of the inorganic core. In specific, there is a reversible transformation, identified by a 140 meV shift in the excitonic energy gap and first order kinetics, between CdS MSCs with distinct compositions and structures (isomers). At the length scale between small molecules and nanocrystals, the transformation of MSCs presents an interesting bridge between molecular isomerization and solid-solid transformation that typify structural transformation in chemistry. Self-assembly of these MSCs has lead to the development of novel properties and emerging optical applications.