FePt nanoparticles (NPs) with thermally responsive array structures were prepared by surface modification with a liquid-crystalline phenylethyl ether-type dendron. Dendron modification was carried out in two steps. In the first step, COOH moieties were introduced on the surface of oleyl-modified FePt NPs by ligand exchange using terminal COOH-substituted -alkyl phosphonic acid. This was followed by the amidation reaction between COOH moieties and the amino-substituted dendron. Infrared spectroscopic measurement and thermogravimetric analysis confirmed that the dendrons were successfully grafted onto the surface of FePt NPs. Transmission electron microscopy also showed an increase in interparticle distance due to dendron modification. Small-angle X-ray scattering (SAXS) revealed that the dendronized NPs pack on an FCC lattice, which melts above 100 °C in thermal response, consistent with the endothermic peak observed in differential scanning calorimetry (DSC). Electron density maps offer detailed insights into the structural organization of the dendronized FePt NP array. These results indicate that the formation of an FCC phase through self-assembly and its thermal transition into a disordered phase enabled dynamic control over magnetic NP arrays. Finally, changes in magnetic properties during thermal phase transition were investigated by a superconducting quantum interference device. The results show certain changes in magnetization behavior introduced by the thermal phase transition. These results demonstrate that dendron modification of FePt NPs enables the introduction of thermal responsiveness in their supramolecular structure and magnetic behavior. The flexible control of magnetic properties is expected to expand the application potential of the magnetic NPs used as building blocks for tunable smart magnetic devices.