The application of graphene cannot be achieved without the processing of its structure. In this work, the graphene nanostructures were processed by particle beam irradiation. Based on the different mechanisms existed during the interaction between different particle beams and graphene, the methods of low energy ion implantation to dope graphene, and particle beam irradiation to join graphene and create graphene nanopore were proposed and studied. Meanwhile, the mechanisms of nanostructures processing were analyzed by atomic simulation methods. Then, the mechanical and electronic transport properties of the nanostructures were analyzed, which laid the foundation for the application of graphene.