Surface coordination chemistry of nanomaterials deals with the chemistry on how ligands are coordinated on their surface metal atoms and influence their properties at the molecular level. This Perspective demonstrates that there is a strong link between surface coordination chemistry and the shape-controlled synthesis, and many intriguing surface properties of metal nanomaterials. While small adsorbates introduced in the synthesis can control the shapes of metal nanocrystals by minimizing their surface energy via preferential coordination on specific facets, surface ligands properly coordinated on metal nanoparticles readily promote their catalysis via steric interactions and electronic modifications. The difficulty in the research of surface coordination chemistry of nanomaterials mainly lies in the lack of effective tools to characterize their molecular surface coordination structures. Also highlighted are several model material systems that facilitate the characterizations of surface coordination structures, including ultrathin nanostructures, atomically precise metal nanoclusters, and atomically dispersed metal catalysts. With the understanding of surface coordination chemistry, the molecular mechanisms behind various important effects (e.g., promotional effect of surface ligands on catalysis, support effect in supported metal nanocatalysts) of metal nanomaterials are disclosed.