Molecular dynamics (MD) simulations of elliptical vibration cutting were conducted in the paper to investigate the correlation between the vibration conditions and the defect mechanism in the material. The interactions between the copper atoms were described by the embedded atom method (EAM) potential, whereas the interactions between the tool and substrate were described by the Morse potential. The elliptical vibration cutting simulation was performed on a Cu (010) surface. With the aid of a visualization technique based on the atomic coordination number, the dislocations and dislocation loops were found to be two prevailing kinds of defects distributed in the substrate. The observations of their evolvement and microstructures were helpful to reveal the material deformation mechanism during the nano-scale vibration machining. In addition, the effects of vibration frequency on the cutting forces were also studied.