In this paper, we demonstrate a new, highly efficient method of crosslinking multilayer graphene, and create nanopores in it by its irradiation with low-energy argon cluster ions. Irradiation was performed by argon cluster ions with an acceleration energy E ≈ 30 keV, and total fluence of argon cluster ions ranging from 1 × 10⁹ to 1 × 10¹⁴ ions/cm². The results of the bombardment were observed by the direct examination of traces of argon-cluster penetration in multilayer graphene, using high-resolution transmission electron microscopy. Further image processing revealed an average pore diameter of approximately 3 nm, with the predominant size corresponding to 2 nm. We anticipate that a controlled cross-linking process in multilayer graphene can be achieved by appropriately varying irradiation energy, dose, and type of clusters. We believe that this method is very promising for modulating the properties of multilayer graphene, and opens new possibilities for creating three-dimensional nanomaterials.