Abstract Crystal phase engineering of inorganic materials is one of the most important strategies for achieving new material properties and functionality. Gold is well known to adopt the face‐centered‐cubic (fcc) structure, and it remains challenging to create new phases, but recent research on nanogold has provided exciting opportunities by achieving 2H (note: H denotes hexagonal), 4H, and body‐centered‐tetragonal (bct) phases. In the current work, an unusual non‐compact phase in 40‐atom gold nanoclusters is reported, which is in contrast to the close‐packed isomer of fcc structure. The non‐compact isomer exhibits exclusive square planes in a layer‐by‐layer stacking, hence giving rise to a unique 0.5 Å channel, whereas the fcc isomer is composed of close‐packed planes with a closed structure (i.e., no 1D channel). The two Au 40 isomers lead to a nearly two orders of magnitude difference in electronic excited‐state lifetime. The attainment of the new non‐compact phase in nanogold presents potential opportunities in terahertz emission owing to the strong electron‐vibration coupling, ion channeling and ion selection, artificial photosynthesis, and biocatalysis.