Molecular dynamics is employed to study the nanoindentation process of Cu50Zr50 amorphous alloy. Deformation behavior of the substrate during indentation process is studied. The effects of indentation depth, loading speed, indenter radius, temperature and adhesion interaction on nanoindentation process are thoroughly investigated. It is found that shear transformation zones constantly migrate and grow during the indentation process. There is no obvious pile-up during indentation process for the indentation depth studied. A bigger indentation depth, loading speed and indenter radius result in a larger load. The indenter radius has no significant effect on the material properties, while a larger loading speed leads to the increase of the material's hardness and elastic modulus. The temperature greatly affects the material's properties. With the increase of temperature, the load and hardness decrease whereas the elastic modulus tends to go up. The hardness is slightly larger when considering the adhesion interaction between indenter and substrate, while the elastic modulus is not significantly affected. (C) 2014 Elsevier B.V. All rights reserved.