In order to understand the nanoscale cutting characteristics of single crystal germanium and improve the optical surface quality of the nanoscale germanium, three-dimensional molecular dynamics (MD) simulations were carried out to study the contact and sliding processes between diamond points and surfaces of single crystal germanium. The material deformation, cutting force, chips pile-up, surface morphology size, and the sliding friction process were investigated. The simulation results show that the cutting force, surface morphology size, and chips plie-up, increase during the contact process with increasing vertical force, and there is no obvious correlation with the cutting speed. The fundamental reason for the fluctuation of the cutting force in the cutting process is caused by the generation of dislocation and the energy fluctuation caused by the destruction of the lattice of single crystal germanium. In order to verify the correctness of the simulation results, nanometer cutting experiments on single crystal germanium were carried out using nano-scratch tester. The experimental results are in agreement with the simulation results, which verify the correctness and effectiveness of the MD model.