Inorganic nanocrystal design has been continuously evolving with a better understanding of the chemical reaction mechanisms between chemical stimuli and nanocrystals. Under certain conditions, molecular compounds can be effective as chemical stimuli to induce transformative reactions of nanocrystals toward new materials that would differ in geometric shape, composition, and crystallographic structure. To explore such evolutionary processes, two-dimensional (2D) layered transition-metal chalcogenide (TMC) nanostructures are an interesting structural platform because they not only exhibit unique transformation pathways due to their structural anisotropy but also present new opportunities for improved material properties for potential applications such as catalysis and energy conversion and storage. The high surface area/volume ratio, interlayer van der Waals (vdW) spacing, and different coordination states between the unsaturated edges and the fully saturated basal planes of the chalcogens are characteristic of 2D layered TMC nanostructures, which subsequently lead to anisotropic chemical processes during chemical transformations, such as regioselective reactions at the interfacial boundaries in the pathways for either porous or solid heteronanostructures. In this Account, we first discuss the chemical reactivity of 2D layered TMC nanostructures. By categorizing the external stimuli in terms of chemical principles, such as Lewis acid–base chemistry, a desirable regioselective chemical reaction can occur with controlled reactivity. In association with the knowledge obtained from the nanoscale chemical reactivity of 2D layered nanocrystals, similar efforts in other important morphologies such as 1D and isotropic 0D nanocrystals are introduced. For instance, for 1D and 0D metal oxide nanocrystals, the effects of molecular stimuli on the atomic-level changes in the crystal lattice are demonstrated, eventually leading to a variety of shape transformations.