The effects of tool rake angle and cutting depth on cutting temperature, cutting force, friction coefficient of rake tool face, atomic accumulation of chip flow and removal, surface quality, sub-surface damage layer thickness, atomic stress, and dislocation evolution were studied by molecular dynamics simulations. The results showed that the cutting temperature was concentrated on the chip, and the chip was easy to flow out with the increase of the tool rake angle, which weakens the extrusion and shearing action of the workpiece, resulting in the gradual reduction of tangential force. The tool rake angle of 10° is beneficial to improve the surface/subsurface quality of the workpiece. The minimum root-mean-square roughness obtained was 0.73 Å. The atomic stress of the workpiece was mainly concentrated around the area of interaction with the tool, and the atoms on the finished surface underwent elastic recovery, so the atomic stress was not significant. The 1/6<112> (Shockley) dislocation density had always been in the leading position, and 1/6<112> (Shockley) dislocation was continuously synthesized and decomposed during the nano-cutting process. With the increase of cutting depth, the number of atoms removed increases rapidly, and the width of chip side flow increases, but the symmetry is weakened. The contour line map even shows deep wave valleys caused by the absence of atoms, which increases the surface roughness. Moreover, the area and depth of the atomic stress distribution in the subsurface layer increase, and the number of amorphous atoms and dislocation density increase.