The invention relates to a preparing method used for utilizing protein to separate and purify nanometer magnetic composite microspheres. The preparing method comprises the following steps of: preparinThe invention relates to a preparing method used for utilizing protein to separate and purify nanometer magnetic composite microspheres. The preparing method comprises the following steps of: preparing magnetic nanoparticles, then adopting a silane coupling agent to modify the surfaces of the nanoparticles, mixing and dispersing the modified particles and high-molecular monomers, a cross linker ang magnetic nanoparticles, then adopting a silane coupling agent to modify the surfaces of the nanoparticles, mixing and dispersing the modified particles and high-molecular monomers, a cross linker and an initiator in water phase containing a surface active agent, carrying out emulsion polymerization and obtaining the magnetic composite microspheres. The prepared nanometer magnetic composite microd an initiator in water phase containing a surface active agent, carrying out emulsion polymerization and obtaining the magnetic composite microspheres. The prepared nanometer magnetic composite microspheres have particle diameters between 50 to 500 nanometers, rich surface function groups, good dispersion stability in medium, high efficiency of immune ligand coupling and strong magnetic responsivspheres have particle diameters between 50 to 500 nanometers, rich surface function groups, good dispersion stability in medium, high efficiency of immune ligand coupling and strong magnetic responsiveness, and are applicable to fast separation and purification of protein in biological samples.eness, and are applicable to fast separation and purification of protein in biological samples.