Small-angle X-ray scattering (SAXS) data reveal that superlattices of organic ligand-stabilized gold (Au) nanocrystals can undergo a series of ordered structure transitions at elevated temperature. An example is presented of a body-centered cubic superlattice that evolves into a hexagonal close-packed structure, followed by the formation of binary simple cubic AB13 and hexagonal AB5 superlattices. Ultimately the superlattice decomposes at high temperature to bicontinuous domains of coalesced Au and intervening hydrocarbon. Transmission electron microscopy revealed that the ordered structure transformations result from partial ligand desorption and controlled Au nanocrystal growth during heating, which forces changes in superlattice symmetry. These observations suggest some similarity between organic ligand-coated nanocrystals and microphase-segregated diblock copolymers, where thermally induced nanophase-segregation of Au and organic ligand influences the ordered arrangements in the superlattice.