To improve the hard and brittle mechanical characteristics of single crystal germanium (Ge), the molecular dynamics (MD) simulation was used to study the mechanism of surface modification on single crystal Ge by ion implantation with three different doses. Results show that the ion implantation causes amorphous phase damage to Ge matrix, and the nano-indentation process shows the lattice evolution. The nano-indentation results reveal that the existence of amorphous phase can reduce the hardness and brittleness of single crystal Ge and enhance its plasticity. Additionally, the degree of amorphous phase damage and the hardness of Ge matrix are related to the ion dose. With increasing the ion dose, the amorphous damage is deepened, and the hardness is decreased.