This study utilizes a hybrid methodology of molecular dynamic simulation and experimental observations to elucidate the intrinsic mechanism through which grain size influences the machined surface quality of pure metallic materials, systematically examining correlations among material removal mechanisms, deformation behavior, and microstructural evolution across varying grain size scales. The results demonstrate that grain size significantly affects machined surface integrity by modifying deformation mechanisms, with its effect strongly linked to a transition in the dominant deformation mechanism from dislocation slip to grain boundary sliding. Transmission electron microscopy characterization confirms that the machined subsurface of pure aluminum metal exhibits amorphous phases and stacking faults, hence corroborating the material deformation mechanism in nanocutting. This study elucidates the formation pathway of distinctive microstructures in nanocutting of pure metallic materials, offering a theoretical foundation for attaining high-precision machining of metallic materials through grain size modulation.