FePt-Ag nanocomposite films with large perpendicular magnetic anisotropy have been fabricated by alternate-atomic-layer electron beam evaporation onto MgO(100) substrates at the low temperature of 300 °C. Their magnetization behavior and microstructure have been studied. The surface topography was observed and varied from continuous to nanogranular microstructures with insertion of Ag nanolayers into Fe/Pt bilayer films. The measurement of angular-dependent coercivity showed a tendency of the domain-wall motion as a typical peak behavior shift toward more like a coherent Stoner-Wohlfarth rotation type with the insertion of Ag nanolayers into the FePt films. On the other hand, the inter-grain interaction was determined from a Kelly-Henkel plot. The FePt film without insertion of Ag nanolayers has a positive δM, indicating strong exchange coupling between neighboring grains, whereas the FePt film with insertion of Ag nanolayers has a negative δM, indicating that inter-grain exchange coupling is weaker, thus leading to the presence of dipole interaction in the FePt–Ag nanogranular films. The magnetic characteristic measurements confirmed that the perpendicular magnetization reversal behavior and related surface morphology of low-temperature-ordered FePt(001) nanogranular films can be systematically controlled by the insertion of Ag nanolayers into the FePt system for next generation magnetic storage medium applications.