Fe3O4 nanoparticles were prepared by coprecipitation method. Microwave synthesis method changed the property of the surface of chitosan, and the carboxymethyl chitosan was prepared. The carboxymethyl chitosan magnetic nanoparticle was prepared by microwave synthesis. Carboxymethyl chitosan magnetic nanoparticles were characterized by IR and SEM methods. The application conditions are discussed. Using this material to separate the alkaloid of Evodia rutaecarpa will greatly shorten the time than traditional separation method. The components will be more pure.