To estimate the effect of bisphosphine ligands on the formation of the isomeric core structures of gold nanoclusters, the different ligation of bisphosphine ligands is usually used to participate in the construction of gold nanoclusters. Here, the selection of the different bisphosphine ligands, DPEphos and Xantphos, is performed to construct two novel gold nanoclusters, [Au11(DPEphos)4Cl2]Cl (1) and [Au11(Xantphos)4Cl2]Cl(2), which have been characterized by IR, 1H and 31P NMR, ESI-MS, XRD, SEM, XPS, TG, UV-vis, and X-ray crystal structure analysis. The structural analyses indicate that the ligation of bisphosphine ligands play a crucial role in the formation of the fascinating Au11 cores: gold nanocluster 1 includes a birdcage-shaped Au11 core with eight electrons, while gold nanocluster 2 contains a crown-shaped Au11 core with eight electrons. Meanwhile, DOS and PDOS studies indicate that the Au11 cores have a strong effect on the composition of HOMO and LUMO orbitals of gold nanoclusters. Furthermore, the different Au11 core structures lead to different optical absorption characteristics (1: 456 nm; 2: 427 nm). All these demonstrate that the ligation of bisphosphine ligands may have an important influence on constructing the stability of the isomeric core structures of gold nanoclusters.