The specific states of aggregation of metal atoms in sub nanometer‐sized gold clusters are related to the different quantum confinement volumes of electrons, leading to novel optical and electronic properties. These volumes can be tuned by changing the relative positions of the gold atoms to generate isomers. Studying the isomeric gold core and the electron coupling between the basic units is fundamentally important for nanoelectronic devices and luminescence; however, appropriate cases are lacking. Here, the structure of the first staggered di‐superatomic Au25‐S was solved using single‐crystal X‐ray diffraction. The optical properties of Au25‐S were studied by comparing with eclipsed Au25‐E. From Au25‐E to Au25‐S, changes in the electronic structures occurred, resulting in significantly different optical absorptions originating from the coupling between the two Au13 modules. Au25‐S shows a longer electron decay lifetime of 307.7 ps before populating the lowest triplet emissive state, compared to 1.29 ps for Au25‐E. The experimental and theoretical results show that variations in the geometric isomerism lead to distinct photophysical processes owing to isomerism‐dependent electronic coupling. This study offers new insights into the connection between the geometric isomerism of nanosized building blocks and the optical properties of their assemblies, opening new possibilities for constructing function‐specific nanomaterials.