The surface chemistry in colloidal nanocrystals on the final crystalline structure of binary superlattices produced by self-assembly of two sets of nanocrystals is hereby demonstrated. By mixing nanocrystals having two different sizes and the same coating agent, oleylamine (OAM), the binary nanocrystal superlattices that are produced, such as NaCl, AlB2, NaZn13, and MgZn2, are well in agreement with the crystalline structures predicted by the hard-sphere model, their formation being purely driven by entropic forces. By opposition, when large and small nanocrystals are coated with two different ligands [OAM and dodecanethiol (DDT), respectively] while keeping all other experimental conditions unchanged, the final binary structures markedly change and various structures with lower packing densities, such as Cu3Au, CaB6, and quasicrystals, are observed. This effect of the nanocrystals coating agents could also be extended to other binary systems, such as AgAu and CoFe2O4Ag supracrystalline binary lattices. In order to understand this effect, a mechanism based on ligand exchange process is proposed. Ligand exchange mechanism is believed to affect the thermodynamics in the formation of binary systems composed of two sets of nanocrystals with different sizes and bearing two different coating agents. Hence, the formation of binary superlattices with lower packing densities may be favored kinetically because the required energetic penalty is smaller than that of a denser structure.