Self-assembled face-centered cubic FePt nanoparticles were embedded into the oxide capping layer using the atomic layer deposition technology. The effect of the oxide-matrix layer on the structure, mono-dispersibility, and magnetic properties of the FePt/oxide composite thin films was investigated. Experimental results suggest that the protection of the oxide-matrix capping layer can effectively inhibit the grain growth and particle aggregation, and preserve the ordered domains of the FePt nanoparticles during the L 1_0 ordering transition through annealing. The combination of the atomic layer deposition capping layer and self-assembled FePt nanoparticles provides a new potential approach to fabricate the ultrahigh-density magnetic recording media.