Revealing structural isomerism in a nanocluster remains significant but challenging. Herein, we have obtained a pair of structural isomers, [Au9Ag12(SR)(4)(dppm)(6)X-6](3+)-C and [Au9Ag12(SR)(4)(dppm)(6)X-6](3+)-Ac [dppm = bis-(diphenyphosphino)methane; HSR = 1-adamantanethiol/tertbutylmercaptan; X = Br/Cl; C stands for one of the structural isomers being chiral; Ac stands for another being achiral], that show different structures as well as different chiralities. These structures are determined by single-crystal X-ray diffraction and further confirmed by high-resolution electrospray ionization mass spectrometry. On the basis of the isomeric structures, the most important finding is the different arrangements of the Au5Ag8@Au-4 metal core, leading to changes in the overall shape of the cluster, which is responsible for structural isomerism. Meanwhile, the two enantiomers of [Au9Ag12(SR)(4)(dppm)(6)X-6](3+)-C are separated by high-performance liquid chromatography. Our work will contribute to a deeper understanding of the structural isomerism in noble-metal nanoclusters and enrich the chiral nanocluster.