It is challenging to develop new top-down approaches to tailor particles into subnanometer size structures on a large scale to further reveal their structure-dependent physicochemical properties. Here, we demonstrate a non-conventional, electrochemical, 3D ion-carving process to tailor particles into subscale flower-like nanostructures at room temperature. The technology is based on the electrochemical insertion/extraction of lithium ions as a carving knife to carve the single-crystalline particle precursor into higher-order, flower-like nanostructures with hexagonal nanopetals as the building units. Our study demonstrates that the morphology of the as-carved, flower-like nanostructures can be controlled by the electrochemical parameters, such as the current density and the number of cycles. Particularly interesting is that dramatically different magnetic properties can be achieved depending on the morphology through careful tuning by the electrochemical ion-carving process. The as-carved, flower-like particles may find many important applications, including magnetic nanodevices. Our approach, in principle, is applicable to prepare various kinds of 3D-structured materials with different compositions.