Structural isomerization is an important concept in organic chemistry and it is recently found to be applicable to thiolated gold nanoparticles. However, to the best of our knowledge, the isomerization with the kernel structure of the cluster changed while maintaining fcc packing was not previously found. Here, we report such a structural isomerization by synthesizing a novel gold nanocluster and solving its atomic structure. The as-obtained novel gold nanocluster Au52(PET)32 (PET = phenylethanethiolate) has completely the same Au/S molar ratio as a well-known gold nanocluster Au52(TBBT)32 (TBBT = 4-tert-butyl-benzenethiolate) but an essentially different fcc structure. As a result of fcc structure isomerization, Au52(PET)32 has remarkably different UV/vis/NIR absorption from Au52(TBBT)32. Another interesting finding in this work is that the kernel of Au52(PET)32 has high-indexed (311)-like facets, which is not previously reported in the structures of gold nanoclusters to the best of our knowledge.