Tool wear not only changes its geometry accuracy and integrity, but also decrease machining precision and surface integrity of workpiece that affect using performance and service life of workpiece in ultra-precision machining. Scholars made a lot of experimental researches and stimulant analyses, but there is a great difference on the wear mechanism, especially on the nano-scale wear mechanism. In this paper, the three-dimensional simulation model is built to simulate nano-metric cutting of a single crystal silicon with a non-rigid right-angle diamond tool with 0 rake angle and 0 clearance angle by the molecular dynamics (MD) simulation approach, which is used to investigate the diamond tool wear during the nano-metric cutting process. A Tersoff potential is employed for the interaction between carbon-carbon atoms, silicon-silicon atoms and carbon-silicon atoms. The tool gets the high alternating shear stress, the tool wear firstly presents at the cutting edge where intension is low. At the corner the tool is splitted along the {1 1 1} crystal plane, which forms the tipping. The wear at the flank face is the structure transformation of diamond that the diamond structure transforms into the sheet graphite structure. Owing to the tool wear the cutting force increases.