Well-defined metallic nanocrystals (NCs) have been explored as effective electrocatalysts for energy conversion and storage technologies (e.g., fuel cell or water splitting). It is commonly known that electrocatalytic performance can be enhanced by controlling composition, size, and surface morphology. In addition, precisely controlling the atomic arrangement inside NCs can improve performance, with their electronic structures being optimized via interfacial coupling. In this review, we summarize recent advances in atomic arrangement engineering approaches of metallic NCs. First, we introduce thermodynamic and kinetic principles to provide a basic understanding on atomic structureproperty correlations. Then, several representative cases of atomic ordering and planar stacking engineering are highlighted for different electrocatalytic processes. Finally, perspectives on the roles of calculations, characterization, and practical applications are outlined.