ConspectusProperties of colloidal semiconductor nanocrystals with a single-crystalline structure are largely dominated by their surface structure at an atomic-molecular level, which is not well understood and controlled, due to a lack of experimental tools. However, if viewing the nanocrystal surface as three relatively independent spatial zones (i.e., crystal facets, inorganic-ligands interface, and ligands monolayer), we may approach an atomic-molecular level by coupling advanced experimental techniques and theoretical calculations.Semiconductor nanocrystals of interest are mainly based on compound semiconductors and mostly in two (or related) crystal structures, namely zinc-blende and wurtzite, which results in a small group of common low-index crystal facets. These low-index facets, from a surface-chemistry perspective, can be further classified into polar and nonpolar ones. Albeit far from being successful, the controlled formation of either polar or nonpolar facets is available for cadmium chalcogenide nanocrystals. Such facet-controlled systems offer a reliable basis for studying the inorganic-ligands interface. For convenience, here facet-controlled nanocrystals refer to a special class of shape-controlled ones, in which shape control is at an atomic level, instead of those with poorly defined facets (e.g., typical spheroids, nanorods, etc).Experimental and theoretical results reveal that type and bonding mode of surface ligands on nanocrystals is facet-specific and often beyond Green's classification (X-type, Z-type, and L-type). For instance, alkylamines bond strongly to the anion-terminated (0001) wurtzite facet in the form of ammonium ions, with three hydrogens of an ammonium ion bonding to three adjacent surface anion sites. With theoretically assessable experimental data, facet-ligands pairing can be identified using density functional theory (DFT) calculations. To make the pairing meaningful, possible forms of all potential ligands in the system need to be examined systematically, revealing the advantage of simple solution systems.Unlike the other two spatial zones, the ligands monolayer is disordered and dynamic at an atomic level. Thus, an understanding of the ligands monolayer on a molecular scale is sufficient for many cases. For colloidal nanocrystals stably coordinated with surface ligands, their solution properties are dictated by the ligands monolayer. Experimental and theoretical results reveal that solubility of a nanocrystal-ligands complex is an interplay between the intramolecular entropy of the ligands monolayer and intermolecular interactions of the ligands/nanocrystals. By introducing entropic ligands, solubility of nanocrystal-ligands complexes can be universally boosted by several orders of magnitude, i.e., up to >1 g/mL in typical organic solvents. Molecular environment in the pseudophase surrounding each nanocrystal plays a critical role in its chemical, photochemical, and photophysical properties.For some cases, such as the synthesis of high-quality nanocrystals, all three spatial zones of the nanocrystal surface must be taken into account. By optimizing nanocrystal surface at an atomic-molecular level, semiconductor nanocrystals with monodisperse size and facet structure become available recently through either direct synthesis or afterward facet reconstruction, implying full realization of their size-dependent properties.