Metal intercalation under graphene has attracted extensive experimental and theoretical research because of its capability to manipulate the electronic structure and properties of graphene. However, the pathways and mechanisms of intercalation are still not well understood. Here, we systematically investigate the intercalation process of metal atoms through graphene vacancies using first-principles calculations. We show that the energy barrier for metal atom penetration through the vacancies in graphene is small as long as the size of the vacancy is larger than a mono-vacancy. However, metal atoms are strongly bonded to the vacancy so that the detachment energy of a metal atom from the vacancy is extremely high. This inhibits the diffusion of the metal atom into the gallery beneath the surface to complete the intercalation process. On the other hand, our calculation results show that the detachment energy of a metal atom from a metal dimer at small vacancy defects is significantly reduced, making intercalation much easier. Therefore, the key step limiting the intercalation process is the detachment of the metal atoms from vacancy defects. This finding from our study provides useful insight into the defect-assisted intercalation mechanism.