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Metal sulfides have been intensively investigated for efficient sodium-ion storage due to their high capacity. However, the mechanisms behind the reaction pathways and phase transformation are still unclear. Moreover, the effects of designed nanostructure on the electrochemical behaviors are rarely reported. Herein, a hydrangea-like CuS microsphere is prepared via a facile synthetic method and displays significantly enhanced rate and cycle performance. Unlike the traditional intercalation and conversion reactions, an irreversible amorphization process is evidenced and elucidated with the help of in situ high-resolution synchrotron radiation diffraction analyses, and transmission electron microscopy. The oriented (006) crystal plane growth of the primary CuS nanosheets provide more channels and adsorption sites for Na ions intercalation and the resultant low overpotential is beneficial for the amorphous Cu-S cluster, which is consistent with the density functional theory calculation. This study can offer new insights into the correlation between the atomic-scale phase transformation and macro-scale nanostructure design and open a new principle for the electrode materials' design., Competing Interests: The authors declare no conflict of interest., (© 2020 The Authors. Published by WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.)