Abstract: Comparing with pristine graphene, graphene with various defects produced by the current technology still has a certain application value. Therefore it is necessary to investigate the influence of defects on graphene properties. In this paper, interaction between carbon atoms that forms the covalent bonds of graphene is modeled with Tersoffff potential, the long range interactions of carbon atoms are characterized by Lennard-Jones potential. The nanoindentation of spherical diamond indenter into defective bilayer graphene is studied by molecular dynamics simulations. The Lernnard-Jones potential function optimal value of cut-o radius is discussed and typical load-depth curves are obtained. The effects including Stone-Thrower-Wales (STW) defect, vacancy (single and double vacancy defects) and hole defect in different positions and numbers on the mechanical properties of graphene are studied. The results show that when defect is in the film's center, it makes intensity decrease significantly; when vacancy defect is in the region covered by indenter, the critical load increases linearly with the increase of distance which is from the defect to the film's center; The more vacancy defect, the lower Young's modulus and intensity. The number of hole defects reaching a certain concentration outside the region covered by indenter radius which makes the mechanical properties of graphene decrease apparently. It is concluded that graphene with the stable structure is not sensitive to small defects and defective graphene still has good performance and practical value.