The intercalation process of iron atoms in the interface between graphene and Ru(0001) was systematically investigated both experimentally and computationally. Scanning tunneling microscopy and low-energy electron diffraction indicate that Fe intercalates at 700 K in the graphene/Ru(0001) system, where the graphene monolayer covers the whole substrate. An atomic-level understanding of the process is achieved using dispersion-corrected density functional theory (DFT) calculation. The results indicate that single-Fe atom intercalation causes only minor energy changes in the system. In contrast, the intercalation of a Fe dimer leads to a considerable drop in the total energy, more than twice the energy change in the case of the single-atom intercalation. In a sequential process, intercalation of the second Fe releases more energy, indicating that once the initial intercalation occurs, the subsequent process is thermodynamically more favored than the first. Combining the experimental observations with theoretical insights from the DFT calculations, we provide a clear picture of Fe intercalation into graphene/Ru(0001), which we believe is of interest to the field of interface and materials science and catalysis.