We report a host-guest chemistry approach to controlling the structures of nanocrystal superlattices through a molecular inclusion process. Upon addition of an appropriate amount of guest molecules such as squalane, polyisoprene, and 4-cyano-4'-pentylbiphenyl into a nanocrystal suspension, the resulting nanocrystal superlattices adopted non-close-packed structures (e.g., from face-centered cubic to body-centered cubic) and changed their morphologies to form superparticles. Our mechanistic studies revealed that these guest molecules can strongly tailor the kinetic process in superlattice formation, resulting in the formation of non-close-packed nanocrystal superlattices. The insights gained in this study are not only important for making nanocrystal superlattices with desirable architectures but also open a new way of synthesizing novel organic/inorganic composite materials.