It is still a challenging task to develop facile top-down methods to carve microparticles into nanostructures on a large scale. We demonstrate a top-down electrochemical method based on a sodium-ion battery system to machine rhombohedral microparticles into hierarchical flower-like nanostructures on a large scale, using Fe₂O₃ as a model. Electrochemical parameters, such as current, and number of cycles can be employed to tune the morphology of the as-derived nanostructures, which can be used to tune magnetization properties. This Na-ion electrochemical nanomachining (ECNM) provides an alternative top-down route to manipulate microparticles into substructures. Particularly interesting, the magnetic properties could be tuned by this ECNM method. It will be interesting to further study electrochemically induced reorganization to change material properties. The concept and methods outlined here could be extended to use other ion-based ECNM, including Mg²⁺, Ca²⁺, Al³⁺, for electrochemical manipulation of structures, opening up additional opportunities for functional materials.