The construction of helical nanosized superstructures has long been a challenging pursuit, and little has been achieved in terms of atomic-level manipulation. Herein, intercluster hierarchical triple-helical structures were presented from all-thiol-stabilized Au6Cu6(4-MeOBT)12 nanoclusters by investigating their structures from both molecular and supramolecular aspects. Based on the atomically precise structure, the mechanism of intercluster assembly was elucidated, and the results indicated an intracluster rotation-induced self-assembly process. Specifically, the presence of abundant intermolecular interactions, including π-π stacking, C-H···O hydrogen bonding, and C-H···π interactions, was found to be beneficial for the organization of the triple-helical superstructure of metal clusters. Moreover, DFT calculations and UV-vis, Raman, and transient absorption measurements were performed to observe the different electronic structures between the nanocluster monomers and helical aggregates. Overall, this work presents an exciting example of the hierarchical triple-helical assembly of atomically precise nanoclusters, which allows an in-depth understanding of complex helical structures/behaviors at the atomic level.