FePt nanoparticles were successfully embedded in a single-crystal MgO matrix using a pulse laser deposition method. The growth behaviors were well controlled and monitored in situ by the reflection high-energy electron diffraction. The FePt nanoparticles and the MgO matrix were grown in three-dimensional island-like and two-dimensional layered modes, respectively. The embedded FePt nanoparticles do not affect the epitaxial growth of MgO layer. The epitaxial relationship between the FePt and MgO is [200](FePt) || [100](MgO). Due to the lattice mismatch between the MgO and FePt, the edge dislocation is observed in the interior of the FePt particles. The study on the structural evolution in the growth process of FePt embedded in the MgO matrix has benefited for not only fundamental research but also the applications of FePt ultrahigh-density perpendicular magnetic recording.