The invention discloses a fucoidan medicinal carrier and a preparation method thereof. Microspheres are prepared from fucoidan and cationic polymers by an electrostatic cross-linking action by utilizing the polyanionic characteristic of the fucoidan, wherein the grain diameters of the microspheres are between 200 nm and 50 mu m. The preparation method of the invention has the characteristics of simple process and convenience operation, does not relate to a toxic organic solvent, is suitable for keeping the activities of small-molecular medicaments and polypeptide protein medicaments, and is an environmental-friendly carrier; and simultaneously, the carrier has an interventional therapy effect because of the materials per se have various biological activities such as coagulation resistance, blood fat reduction, tumor resistance, virus resistance, body immune function enhancement and the like. Therefore, the carrier has the characteristics of high practicability and wide application prospect.