Dual layers of Pt and Fe, deposited sequentially onto highly oriented pyrolytic graphite (HOPG), were annealed under ultrahigh vacuum, from room temperature to 560 °C. The formation of FePt alloy NPs, through interdiffusion, was studied by in situ X-ray photoelectron spectroscopy (XPS), ex situ atomic force (AFM), and high-resolution transmission electron (TEM) microscopies. With increasing annealing temperature, the Pt 4f7/2 binding energy shifts positively, and the positions of the Pt 5d-6s valence band centers move away from the Fermi level and broaden. Between 300 and 400 °C, Fe and Pt atoms diffuse significantly. Simultaneously, a surface chemical reaction occurs between metal oxide and adventitious carbon on the NP surface, resulting in the disappearance of the O 1s spectrum and the formation of an amorphous hydrocarbon shell. At elevated temperatures, the shell is continually lost, through fragmentation, and replaced by a new hydrocarbon from the vacuum background, assuring that the NPs do not coalesce during the whole annealing process. Stable FePt alloy NPs are formed on the HOPG surface as the annealing temperature is increased to ∼400 °C (A1 structure) and ∼500 °C (L10 structure). A continual Pt surface enrichment occurs with increasing annealing temperature, even before the formation of stable L10 NPs, resulting in the formation of a Pt-rich layer around the NPs. On the basis of the mass balance in the system, an Fe-rich layer must lie below the Pt-rich layer, surrounding the L10 core.