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In recent years, the use of the multilayer graphene sheets has been considered more than the single-layer due to the cost-effectiveness and the possibility of mass production. But this type of graphene has some kind of structural weakness due to the weak physical link between its layers. Then, in order to strengthen, many structural modifications are proposed by various techniques to manage the mechanisms at interlayer distances. In this study, the focused ion beam irradiation method has been examined to cross-link and strengthen multi-layer graphene sheets with the help of the molecular dynamics simulation technique. Then, uniaxial and transverse tensile tests were performed to check the mechanical properties of obtained cross-linked multilayer graphene sheets. The results of this research can be considered for the creation of a new class of graphene structures. Such structures could be implemented as a membrane in water desalination or as a storage foam in hydrogen or carbon dioxide storage.