Nanocrystals and their ordered arrays hold many important applications in fields such as catalysis, surface-enhanced Raman spectroscopy based sensors, memory storage, and electronic and optical nanodevices. Herein, a simple and general method to synthesize ordered, three-dimensional, transparent gold nanocrystal/silica superlattice thin films by self-assembly of gold nanocrystal micelles with silica or organosilsesquioxane by spin-coating is reported. The self-assembly process is conducted under acidic sol–gel conditions (ca. pH 2), ensuring spin-solution homogeneity and stability and facilitating the formation of ordered and transparent gold nanocrystal/silica films. The monodisperse nanocrystals are organized within inorganic host matrices as a face-centered cubic mesostructure, and characterized by transmission electron spectroscopy and X-ray diffraction.