Molecular dynamics is a rapidly developing field of science and has become an established tool for studying the dynamic behavior of material machining. A three-dimensional molecular dynamics (MD) model about the atoms of the diamond cutting tools and the diamond grits is built by using the molecular dynamics. The Tersoff potential function is used to calculate the force and potential energy among the atoms of the diamond tools and the atoms of the diamond grits. The lapping processes at a special cutting depth are simulated. The variety of the specimen potential energy in the lapping process is observed. The mechanism of the diamond micro machining and the form of the surface formation are given by comparing the distribution maps of atoms in initial and cutting states. This study will give a strong support to the diamond cutting tools’ lapping.