With continuous research efforts devoted into synthesis and characterization chemistry of functional nanomaterials in the past decades, the development of metal materials is stepping into a new era, where atom-by-atom customization of property-dictating structural attributes is expected. Herein, the state-of-the-art modulation of functional metal nanomaterials at the atomic level, by size- and structure-controlled synthesis of thiolate-protected metal (e.g., Au and Ag) nanoclusters (NCs), is exemplified. Metal NCs are ultrasmall (<3 nm) particles with hierarchical primary, secondary, and tertiary structures, reminiscent of natural proteins or enzymes. Given the proven dependence of their physicochemical properties on their size and structure, documented synthetic methodologies delivering NCs with atomic-level monodispersity and tailorable size and structural attributes at individual hierarchical levels are categorized and discussed. Such assured atomic-level modulation could confer metal NCs with novel application opportunities in diverse fields, which are also exemplified by their size- and structure-dictated catalytic and biomedical performance. The precise synthesis and application chemistry developed based on the hierarchical structure scheme of metal NCs could increase the acceptance of metal NCs as a new family of functional materials.