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Monodispersive FePt magnetic nanoparticles (NPs) with hydrophobic ligand were chemically synthesized and with controllable surface-functional properties. In order to compare and obtain the high saturation magnetization of FePt NPs, the synthesized solvents were changed from octyl to phenyl ether leading to effectively increase magnetization due to the increased particle size and isolated distance of each NPs. The surface modification of FePt NPs by using mercaptoacetic acid (thiol) and 11-mercaptoundecanoic acid (MUA) as a phase transfer reagent through ligand-exchange turned the NPs hydrophilic, and the FePt NPs were water-dispersible. Transmission electron microscopy images indicate that the NPs are slightly agglomerate after ligand-exchange. Fourier transform infrared spectroscopy (FTIR) spectra suggest that thiol and MUA functional group bond to the FePt atoms of the surface. The water-dispersible FePt NPs used as heating agents could reach the demand of biocompatibility and provide heat response for magnetically induced hyperthermia in biological fields.