Structural isomerism of colloidal semiconductor nanocrystals has been largely unexplored. Here, we report one pair of structural isomers identified for colloidal nanocrystals which exhibit thermally-induced reversible transformations behaving like molecular isomerization. The two isomers are CdS magic-size clusters with sharp absorption peaks at 311 and 322 nm. They have identical cluster masses, but slightly different structures. Furthermore, their interconversions follow first-order unimolecular reaction kinetics. We anticipate that such isomeric kinetics are applicable to a variety of small-size functional nanomaterials, and that the methodology developed for our kinetic study will be helpful to investigate and exploit solid-solid transformations in other semiconductor nanocrystals. The findings on structural isomerism should stimulate attention toward advanced design and synthesis of functional nanomaterials enabled by structural transformations.