Biocompatible magnetic protein microcapsules (MPMCs) were prepared by sonochemical method. Under high intensity ultrasonic treatment, the MPMCs were yielded at the interface between the oil liquids containing Fe3O4 nanoparticles and the protein solution within several minutes. Meanwhile, the hydrophobic drugs could be loaded into MPMCs directly via sonochemical method and the activities of proteins and drugs were not destroyed. The sonochemical technique is a very simple and cost-effective method to fabricate MPMCs as drug carriers. Such prepared MPMCs are very promising carriers for drug delivery systems and magnetic resonance imaging.