Graphene, a two-dimensional material with honeycomb lattice, has attracted great attention from the communities of fundamental research and industry, due to novel phenomena such as quantum Hall effect at room temperature, Berry phase, and Klein tunneling, and excellent properties including extremely high carrier mobility, high Young's modulus, high thermal conductivity and high flexibility. Some key issues hinder graphene from being used in electronics, including how to integrate it with Si, since Si based technology is widely used in modern microelectronics, and how to place high-quality large area graphene on semiconducting or insulating substrates. A well-known method of generating large-area and high-quality graphene is to epitaxially grow it on a single crystal metal substrate. However, due to the strong interaction between graphene and metal substrate, the intrinsic electronic structure is greatly changed and the conducting substrate also prevents it from being directly used in electronics. Recently, we have developed a technique, which intercalates silicon between epitaxial graphene and metal substrate such as Ru (0001) and Ir (111). Experimental results from Raman, angle-resolved photoemission spectroscopy, and scanning tunneling spectroscopy confirm that the intercalation layer decouples the interaction between graphene and metal substrate, which results in the recovery of its intrinsic band structure. Furthermore, we can use this technique to intercalate thick Si beyond one layer and intercalate Si between graphene and metal film, which indicates the possibility of integrating both graphene and Si device and vast potential applications in industry by reducing its cost. Besides Si, many other metal elements including Hf, Pb, Pt, Pd, Ni, Co, Au, In, and Ce can also be intercalated between graphene and metal substrate, implying the universality of this technique. Considering the versatility of these elements, we can expect this intercalation technique to have wide applications in tuning graphene properties. We also investigate the intercalation mechanism in detail experimentally and theoretically, and find that the intercalation process is composed of four steps:creation of defects, migration of heteroatoms, self-repairing of graphene, and growth of intercalation layers. The intercalation of versatile elements with different structures by this technique provides a new route to the construction of graphene heterostructures, espectially van der Waals heterostructure such as graphene/silicene and graphene/hafnene, and also opens the way for placing graphene on insulating substrate for electronic applications if the intercalation layer can be oxidized by further oxygen intercalation.