Two diphosphine-protected superatom gold selenido nanoclusters, [Au₈Se₂(dppm)₄]²⁺ (SD/Au8a, dppm = Ph₂PCH₂PPh₂) and [Au₈Se₂(dppe)₄]²⁺ (SD/Au8b, dppe = Ph₂P(CH₂)₂PPh₂), were obtained by the reduction of [Au(SMe₂)Cl] in the presence of Ph₃PSe as the selenium ion releasing agents. Both can be regarded as "superatoms" with 1S² configuration based on the spherical Jellium model. Despite the same metal–ligand binding motifs on the surface and the intrinsic C₂ molecular symmetry, the configurations of Au₈Se₂ kernels in them are different in terms of Au–Au bonded metallic frameworks. SD/Au8a displays a heart-shaped [core + exo] type structure (Au₄ tetrahedron core + two exo Au₂Se units), whereas the two exo Au₂Se counterparts in SD/Au8b are additionally locked by an obvious Au–Au bond, forming a distorted hexagonal Au₆ ring with two capping AuSe units appended above and below it. Consequently, they showed different photophysical properties as reflected by their electronic absorption and emission spectra. Especially, both SD/Au8a and SD/Au8b exhibit blue-shifted thermochromic luminescence upon cooling from 293 to 83 K but the latter exhibits anomalous emission intensity evolution trends due to the occurrence of temperature-induced phase transition as revealed by varied-temperature crystallographic analyses. This work not only clearly illustrates the significance of ligands on tuning the kernel structure but also provides two rarely comparable examples for better understanding of the structure-property relationship of gold nanoclusters.