Single-crystal silicon (Si) has important applications in semiconductor, infrared optics, and photovoltaic industries. However, Si is difficult to be machined precisely due to its hard and brittle characteristics. Ion irradiation is proposed as an advanced technology to reduce the hardness and brittleness for a covalent crystal, which is beneficial for the ductile machining process. In the present research, the simulation and experimental investigation of Si with Au ion irradiation were carried out firstly. As following, the grooving experiment is carried out by elliptical vibration cutting (EVC). the machining performance is compared with ordinary cutting (OC) and the material removal mechanism is elaborated. The critical depth of cut for brittle-to-ductile transition is nearly 7 times higher by EVC compared to OC. Initial verification of material modification was conducted by Raman spectra and cutting microgrooves. Finally, the ion irradiation damage mechanism and amorphous Si (a-Si)/crystalline Si (c-Si) machining deformation mechanism were analyzed in detail by transmission electron microscopy. The irradiated sample contains an amorphous layer of 1050 nm, a transition layer containing dislocations and nanocrystals, and a fully crystalline layer. During machining a-Si/c-Si interface, the machining defects in the amorphous layer will first absorb the energy and ensure that the crystalline layer does not produce subsurface damage. In summary, ion-irradiated Si can be achieved in the amorphous region at any depth position and the substrate ductile machining without subsurface damage generation by EVC.