The invention discloses a porous magnetic starch microsphere and a preparation method thereof. The method is characterized in that organic peroxide-surface modified Fe3O4 magnetic particle is used as a nucleus, mineral oil is used as a continuous phase, starch molecules and the magnetic nucleus are combined through reversed-phase polymerization reaction to form a magnetic starch micro sol particle with a nuclear-shell structure, the starch molecules on a shell layer are subjected to cross-linking reaction under the action of cross-linking agent-epoxy chloropropane, so that the magnetic starch micro sol is gelatinized to obtain magnetic starch micro gel, then the magnetic starch micro gel is subjected to demulsification, washing, magnetic separation, supercritical CO2 extraction and drying to obtain the porous magnetic starch microspheres. The porous magnetic starch microsphere is round, has uniform particle size, narrow pore size distribution, large specific surface and high mechanical strength, and the porous magnetic starch has a magnetic guiding function and a flexible and strong adsorption loading function, and has wide application prospect in the fields of sewage treatment, targeted drugs, catalytic industry, environment monitoring, immobilized enzymes and the like.