Understanding the structural behavior of graphene flake, which is the structural unit of bulk crumpled graphene, is of high importance, especially when it is in contact with the other types of atoms. In the present work, crumpled graphene is considered as storage media for two types of nanoclusters—nickel and hydrogen. Crumpled graphene consists of crumpled graphene flakes bonded by weak van der Waals forces and can be considered an excellent container for different atoms. Molecular dynamics simulation is used to study the behavior of the graphene flake filled with the nickel nanocluster or hydrogen molecules. The simulation results reveal that graphene flake can be considered a perfect container for metal nanocluster since graphene can easily cover it. Hydrogen molecules can be stored on graphene flake at 77 K, however, the amount of hydrogen is low. Thus, additional treatment is required to increase the amount of stored hydrogen. Remarkably, the size dependence of the structural behavior of the graphene flake filled with both nickel and hydrogen atoms is found. The size of the filling cluster should be chosen in comparison with the specific surface area of graphene flake.