The invention relates to a method for transferring magnetic nano-particles from an oil phase to an aqueous phase. The method comprises the steps of adding an oxidant to an oil-phase magnetic nano-particle solution, oxidizing unsaturated carbon-carbon double bonds in an oleic-acid long chain on the surfaces of oil-phase magnetic nano-particles into hydrophilic carboxyl groups through reaction, andtransforming the oil-phase dispersed magnetic nano-particles into aqueous-phase dispersed magnetic nano-particles. The method is simple in process, convenient and fast to operate, effectively reducesthe cost for cleaning the oil-phase magnetic nano-particles, realizes the surface carboxyl functional modification of the magnetic nano-particles, and ensures that introduced carboxyl functional groups can be connected to proteins, nucleic acids, medicaments and the like, thereby enabling the magnetic nano-particles to be applied in the field of biological medicines better.